{ "source_file": "multiqc_general_stats.txt", "total_samples": 480, "metrics": [ "Sample", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30", "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct", "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean", "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm", "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm", "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median", "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean", "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION", "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES", "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES", "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent", "STAR_mqc-generalstats-star-uniquely_mapped_percent", "STAR_mqc-generalstats-star-uniquely_mapped", "fastp_mqc-generalstats-fastp-pct_duplication", "fastp_mqc-generalstats-fastp-after_filtering_q30_rate", "fastp_mqc-generalstats-fastp-after_filtering_q30_bases", "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads", "fastp_mqc-generalstats-fastp-after_filtering_gc_content", "fastp_mqc-generalstats-fastp-pct_surviving", "fastp_mqc-generalstats-fastp-pct_adapter", "Kallisto_mqc-generalstats-kallisto-fragment_length", "Kallisto_mqc-generalstats-kallisto-percent_aligned", "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads", "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates", "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc", "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length", "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length", "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails", "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails", "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences" ], "samples": [ { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 122711241, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 369722048, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007169, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.622924, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 139413426, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.904136, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.935307, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.076852, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.064693, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 126048684, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 63426395, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10714150, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4387071, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 218.676205, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 111, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.696242, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.521597, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975565, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 138.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 131, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.22, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.39, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 145, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 247.51841699999997, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.627422, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.0619, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.56889517955341, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.24, "STAR_mqc-generalstats-star-uniquely_mapped": 176063788, "fastp_mqc-generalstats-fastp-pct_duplication": 44.2968, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974429, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 46200464259, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 369722048, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.537661, "fastp_mqc-generalstats-fastp-pct_surviving": 98.45613266730075, "fastp_mqc-generalstats-fastp-pct_adapter": 63.14957426506653, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 138.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.36494102726597, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 179989827, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.84385753189846, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 187759786, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.07530115581326, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 187759786, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.85933160339066, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.15540680982056, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 184861024, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 80.85933160339066, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.15540680982056, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 184861024 }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.2669114574467, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.307819586675, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 184861024, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 81.2669114574467, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.307819586675, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 184861024 }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 86764997, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 405102760, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007181, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.775403, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 90984870, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.861515, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.904945, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.106513, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.095055, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 78384794, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 39425832, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 9691029, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4141264, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 131.760265, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 63, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.627891, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.391099, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975624, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 136.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 129, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.35, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.44, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.16, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.69, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 143, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 241.94232299999996, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.781011, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.053, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.21363075874568, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.17, "STAR_mqc-generalstats-star-uniquely_mapped": 192772813, "fastp_mqc-generalstats-fastp-pct_duplication": 59.277, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974548, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 50196479419, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 405102760, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.544812, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43591236420505, "fastp_mqc-generalstats-fastp-pct_adapter": 64.47685666215354, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 136.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.2869619550358, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 197056084, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.07404182273032, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 205769800, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.02250111371858, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 205769800, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.12855056282567, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.06072749541376, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 202551380, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.12855056282567, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.06072749541376, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 202551380 }, { "Sample": "659_6i-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.21572717918839, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.21801788760955, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 202551380, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.21572717918839, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.21801788760955, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 202551380 }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 99602868, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 451678338, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008155, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.764551, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 106347390, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.868842, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.9163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.096522, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.0837, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 92399065, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 46517372, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10264871, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4249166, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 161.299414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 71, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.635336, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.429582, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974517, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 140.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 132, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.32, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.43, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.72, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 150, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 261.255122, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.770837, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.5471, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.71501888842299, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.31, "STAR_mqc-generalstats-star-uniquely_mapped": 212995095, "fastp_mqc-generalstats-fastp-pct_duplication": 56.0454, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973312, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 56780879063, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 451678338, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.548388, "fastp_mqc-generalstats-fastp-pct_surviving": 98.4320171763979, "fastp_mqc-generalstats-fastp-pct_adapter": 60.463191291495974, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 140.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.28312053787268, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 219703391, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.10882462776824, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 229436697, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.05742824866945, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 229436697, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.16573441045566, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.07431828178574, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 225839169, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.16573441045566, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.07431828178574, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 225839169 }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.28877497917597, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.22799042003206, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 225839169, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.28877497917597, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.22799042003206, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 225839169 }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 56455296, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 337284940, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008266, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.849755, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 50675435, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.812521, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.878418, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.132462, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.121582, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 41174847, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 20720143, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 6712554, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2867885, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 72.231219, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 30, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.503639, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.214489, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974442, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 143.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 135, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.41, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 154, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 273.914271, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.856838, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.36240000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.44333040617745, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.24, "STAR_mqc-generalstats-star-uniquely_mapped": 158926505, "fastp_mqc-generalstats-fastp-pct_duplication": 64.4351, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973193, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 42635870190, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 337284940, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.552691, "fastp_mqc-generalstats-fastp-pct_surviving": 98.118526840784, "fastp_mqc-generalstats-fastp-pct_adapter": 58.37797736553241, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 143.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.95350168910595, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 163504780, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.83246774143427, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 171876276, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.36159658825807, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 171876276, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.93288216742016, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.8068345239488, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168642470, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.93288216742016, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.8068345239488, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 168642470 }, { "Sample": "659_Dl-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.74389956458344, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.96072378446544, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168642470, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.74389956458344, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.96072378446544, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 168642470 }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 197751475, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 472731300, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005589, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.56651, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 204924135, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.93071, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.956607, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.056397, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.043393, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 190724878, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 95997343, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11557004, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4354587, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 346.652517, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 158, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.712096, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.579266, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975848, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 138.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 130, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.35, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.56, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 151, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 346.768174, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.569695, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6486, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.52260343944634, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.92, "STAR_mqc-generalstats-star-uniquely_mapped": 226722204, "fastp_mqc-generalstats-fastp-pct_duplication": 38.6836, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974798, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 58573251308, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 472731300, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.535287, "fastp_mqc-generalstats-fastp-pct_surviving": 98.46464150341733, "fastp_mqc-generalstats-fastp-pct_adapter": 63.49954395997476, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 138.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.21867094478407, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 232155200, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.330464659752, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 240051298, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.68285766396423, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 240051298, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.38607921236309, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.01870700755376, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 236365650, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.38607921236309, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.01870700755376, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 236365650 }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.90758998367436, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.18111313551694, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 236365650, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.90758998367436, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.18111313551694, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 236365650 }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 134657805, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 525908288, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005454, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.677632, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 169536169, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.916894, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.947381, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.066187, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.052619, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 155446647, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 78245827, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11221158, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4345904, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 280.844642, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 125, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.689891, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.540849, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975816, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 139.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 131, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.35, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 154, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 359.279327, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.681348, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6483, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.55596912855111, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.96, "STAR_mqc-generalstats-star-uniquely_mapped": 252337753, "fastp_mqc-generalstats-fastp-pct_duplication": 47.702299999999994, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974771, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 65528247264, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 525908288, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.536988, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49101815211236, "fastp_mqc-generalstats-fastp-pct_adapter": 62.49314286523112, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 139.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.21042561702316, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 258248384, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.37535276197477, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 266982867, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.32470298049513, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 266982867, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.41807263027368, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.73844080586157, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 262954144, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.41807263027368, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.73844080586157, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 262954144 }, { "Sample": "659_Lx-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.55266539861093, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.89624050572102, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 262954144, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.55266539861093, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.89624050572102, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 262954144 }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 175254736, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 410870718, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006706, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.574837, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 174687175, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.918194, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.949235, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.066032, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.050765, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 160396784, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 80959307, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11534912, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4329733, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 312.735042, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.702346, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.563006, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975311, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 151.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 142, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.29, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 170, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 333.404403, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.578718, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.6801, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.16462277738556, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.88, "STAR_mqc-generalstats-star-uniquely_mapped": 194916266, "fastp_mqc-generalstats-fastp-pct_duplication": 42.838300000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974247, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 53690661557, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 410870718, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.541057, "fastp_mqc-generalstats-fastp-pct_surviving": 98.542564564574, "fastp_mqc-generalstats-fastp-pct_adapter": 51.195705574969594, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 151.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.42284481806269, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 200140971, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.039455165281, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 208473729, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.74505087008463, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 208473729, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.07309039798578, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.06842825922678, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 205435359, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.07309039798578, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.06842825922678, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 205435359 }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.80581080338301, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.1752840902135, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 205435359, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.80581080338301, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.1752840902135, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 205435359 }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 108569758, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 487609194, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006655, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.761098, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 116490707, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.87819, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.921322, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.093951, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.078678, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 102301002, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 51593736, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10944439, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4405970, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 190.097097, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 81, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.647195, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.457287, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974362, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 147.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 137, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.84, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.32, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 163, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 315.379243, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.766198, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.66120000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 86.76959655347147, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.81, "STAR_mqc-generalstats-star-uniquely_mapped": 231149922, "fastp_mqc-generalstats-fastp-pct_duplication": 56.752199999999995, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973276, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 62457636060, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 487609194, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546408, "fastp_mqc-generalstats-fastp-pct_surviving": 98.44048262754676, "fastp_mqc-generalstats-fastp-pct_adapter": 55.25877473861507, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 147.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.41369232672837, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 237499060, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.33018897329931, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 247667007, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.18396412561587, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 247667007, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.38584168832425, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.53506413580874, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 243804597, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.38584168832425, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.53506413580874, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 243804597 }, { "Sample": "659_Mt-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.42532560929908, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.66417177523522, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 243804597, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.42532560929908, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.66417177523522, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 243804597 }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 84571576, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 482784100, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008407, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.826382, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 83820050, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.824633, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.882615, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.126947, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.117385, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 69120750, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 34727617, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10640692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4618681, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 115.570767, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 29, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.496329, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.270278, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973384, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 133.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 127, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.24, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.86, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.4, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 138, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 205.951637, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.833388, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.22699999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.01618337463171, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.9, "STAR_mqc-generalstats-star-uniquely_mapped": 229086587, "fastp_mqc-generalstats-fastp-pct_duplication": 57.760999999999996, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97194, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 58875373308, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 482784100, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.596663, "fastp_mqc-generalstats-fastp-pct_surviving": 98.16374759044083, "fastp_mqc-generalstats-fastp-pct_adapter": 65.86101858050847, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 133.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.14258775299352, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 234494484, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.8510984600925, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 245907533, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.33702808734827, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 245907533, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.95640635400324, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.35951999247696, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 241392050, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.95640635400324, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.35951999247696, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 241392050 }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.78902283212253, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.56791091504464, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 241392050, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.78902283212253, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.56791091504464, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 241392050 }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 40766331, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 214549178, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008606, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.832265, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 35987478, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.811692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.872254, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.136999, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.127746, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 29210747, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 14670108, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 4930256, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2148507, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 49.142919, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 11, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.32793, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.116306, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.972692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 140.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 133, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.25, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.97, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.42, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 147, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 227.981542, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.83949, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.03439999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.0953426293948, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.9, "STAR_mqc-generalstats-star-uniquely_mapped": 101800299, "fastp_mqc-generalstats-fastp-pct_duplication": 60.9289, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971263, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 26844909276, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 214549178, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.600534, "fastp_mqc-generalstats-fastp-pct_surviving": 97.97856767818656, "fastp_mqc-generalstats-fastp-pct_adapter": 61.186184003623936, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 140.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.98188170173275, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 104036915, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.81648670002772, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 109487811, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.14586269525276, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 109487811, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.8790376211081, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.72641932937165, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 107274589, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.8790376211081, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.72641932937165, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 107274589 }, { "Sample": "659_bCu-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.59655875883234, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.90878844569613, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 107274589, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.59655875883234, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.90878844569613, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 107274589 }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 343547875, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590748766, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005864, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.496974, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 297162172, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.943477, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.972368, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.044865, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.027632, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 280365566, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 141693485, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13332279, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4026596, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 574.622526, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 259, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.748546, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.640886, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974515, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 155.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.24, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.65, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.07, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.96, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 216, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 555.679947, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.499905, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.95270000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.31389278557182, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.45, "STAR_mqc-generalstats-star-uniquely_mapped": 281937681, "fastp_mqc-generalstats-fastp-pct_duplication": 36.2366, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973471, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77605458065, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590748766, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.550485, "fastp_mqc-generalstats-fastp-pct_surviving": 98.45812766666666, "fastp_mqc-generalstats-fastp-pct_adapter": 48.472439, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 155.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.36571575673845, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290547126, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.18255027919378, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 471615201, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.36424385891371, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 471615201, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.12503568282985, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.8883027408643, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295374383, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.12503568282985, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.8883027408643, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295374383 }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.6097527425441, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.99419387022468, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295374383, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.6097527425441, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.99419387022468, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295374383 }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 224392019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590952262, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006005, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.582331, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 246822387, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.935578, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.968187, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.050044, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.031813, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 230921672, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 116782548, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12352002, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3837285, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 467.524572, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 200, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.729182, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.607829, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974224, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 154.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 142, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.31, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.05, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 218, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 544.219773, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.585849, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.92490000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.06339491402406, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.4, "STAR_mqc-generalstats-star-uniquely_mapped": 281881279, "fastp_mqc-generalstats-fastp-pct_duplication": 42.328700000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973158, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77219251156, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590952262, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.558526, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49204366666666, "fastp_mqc-generalstats-fastp-pct_adapter": 48.798441, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 154.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.27448160271193, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290377636, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.2719403550148, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 532548376, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.30340172840135, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 532548376, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.40589614577979, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.21301719630273, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295476131, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.40589614577979, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.21301719630273, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295476131 }, { "Sample": "659_bGW-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.89456969469921, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.32075034852815, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295476131, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.89456969469921, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.32075034852815, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295476131 }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 202638424, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590321106, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006475, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.617614, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 225730634, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.922593, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.955532, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.060473, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.044468, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 208257496, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 105089882, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13650576, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4890601, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 392.923792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.741624, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.609797, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975094, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 146.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 136, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.92, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.82, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 167, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 372.700817, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.621639, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.202, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.57778592678132, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.93, "STAR_mqc-generalstats-star-uniquely_mapped": 283136242, "fastp_mqc-generalstats-fastp-pct_duplication": 44.440400000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974006, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75291221306, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590321106, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.556788, "fastp_mqc-generalstats-fastp-pct_surviving": 98.386851, "fastp_mqc-generalstats-fastp-pct_adapter": 56.44384483333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 146.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.06540882853001, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289450403, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.07577247781306, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 319244665, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.31587627425279, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 319244665, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.61777449234852, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.86917021394794, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295160553, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.61777449234852, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.86917021394794, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295160553 }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.10347774094294, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.00977816978138, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295160553, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.10347774094294, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.00977816978138, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295160553 }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 135826535, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590718792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006373, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.744583, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 150879924, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.899913, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.942248, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.075134, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.057752, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 135778797, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 68570997, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11336233, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4202825, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 256.785351, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.697874, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.532198, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97488, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 151.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 141, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.96, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.41, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 183, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 433.913234, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.749358, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1228, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.91443143775646, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.03, "STAR_mqc-generalstats-star-uniquely_mapped": 283632497, "fastp_mqc-generalstats-fastp-pct_duplication": 58.5416, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973859, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76534807998, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590718792, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.555894, "fastp_mqc-generalstats-fastp-pct_surviving": 98.453132, "fastp_mqc-generalstats-fastp-pct_adapter": 52.60127799999999, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 151.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.96097362008419, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289336940, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.8753848965766, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361712582, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.8649009119912, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361712582, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.64203793175619, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.97406937749832, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295359396, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.64203793175619, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.97406937749832, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295359396 }, { "Sample": "659_bGc-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.90030958404614, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.0913079704429, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295359396, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.90030958404614, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.0913079704429, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295359396 }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 233117319, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589893144, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006225, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.583955, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 245422175, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.929308, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.96519, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055729, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.03481, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 228072907, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 115597877, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13677128, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4169032, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 469.802865, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 207, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.74129, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.617214, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973489, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 158.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 145, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.83, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 224, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 582.337348, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.587613, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.4991, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.27852406430924, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.75, "STAR_mqc-generalstats-star-uniquely_mapped": 282421131, "fastp_mqc-generalstats-fastp-pct_duplication": 43.293, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972446, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77582863950, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589893144, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.560321, "fastp_mqc-generalstats-fastp-pct_surviving": 98.315524, "fastp_mqc-generalstats-fastp-pct_adapter": 46.79430583333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 158.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.20997004162503, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289666940, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.06991740559299, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 331530446, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.57223739970475, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 331530446, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.4237827231286, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.18493256466803, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294946572, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.4237827231286, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.18493256466803, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294946572 }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.2225840071315, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.29546840096856, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294946572, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.2225840071315, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.29546840096856, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294946572 }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 183950262, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590472974, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005925, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.639271, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 213000606, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.924412, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.961991, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.059163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.038009, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 196900332, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 99782497, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12601766, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3942493, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 406.121508, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 184, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.730404, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.601475, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975155, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 160.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 146, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.56, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.2, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.84, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 233, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 623.487796, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.643081, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.4576, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.64612138750879, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.89, "STAR_mqc-generalstats-star-uniquely_mapped": 283106606, "fastp_mqc-generalstats-fastp-pct_duplication": 49.3811, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974181, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77857436892, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590472974, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553017, "fastp_mqc-generalstats-fastp-pct_surviving": 98.41216233333333, "fastp_mqc-generalstats-fastp-pct_adapter": 45.868462, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 160.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.185949828078, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289880749, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.98787112768102, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 323132553, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.08462120176148, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 323132553, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.49419147746981, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.2901178505081, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295236487, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.49419147746981, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.2901178505081, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295236487 }, { "Sample": "659_bNS-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.83616775582847, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.39885719816195, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295236487, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.83616775582847, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.39885719816195, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295236487 }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 194376101, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 540201404, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008505, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.591874, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 220470439, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.922913, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962312, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.056249, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037688, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 203475014, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 102962826, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12401222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4032472, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 415.352489, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 187, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.730105, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.60342, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974846, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 159.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.11, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.86, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 208, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 476.274649, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.59695, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.9713, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.85484671619318, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.17, "STAR_mqc-generalstats-star-uniquely_mapped": 257053633, "fastp_mqc-generalstats-fastp-pct_duplication": 44.6957, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973848, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 71731290524, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 540201404, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.562319, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49856126833085, "fastp_mqc-generalstats-fastp-pct_adapter": 45.82741796491517, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 159.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.75437495901066, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 264035253, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.31264232402926, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 274217916, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.83023728385194, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 274217916, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.32613640000454, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.2968764257414, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270100702, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.32613640000454, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.2968764257414, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 270100702 }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.94610823981549, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.39308308054675, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270100702, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.94610823981549, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.39308308054675, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 270100702 }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 131323217, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590311358, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007508, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.737822, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 154766623, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.90068, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.949678, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.070683, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.050322, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 139395180, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 70577981, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10939414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3739830, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 279.59464, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 118, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.688182, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.530884, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973833, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 163, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.42, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.39, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.94, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 225, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 519.382924, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.743403, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.9102, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.09215048939973, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.32, "STAR_mqc-generalstats-star-uniquely_mapped": 281353113, "fastp_mqc-generalstats-fastp-pct_duplication": 58.3558, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.9728, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79145586002, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590311358, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.566749, "fastp_mqc-generalstats-fastp-pct_surviving": 98.38522633333334, "fastp_mqc-generalstats-fastp-pct_adapter": 42.71195066666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 163, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.64035914077736, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288191065, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.83227886225762, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 398904753, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.58492857921108, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 398904753, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.99373180254821, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.77339506654047, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295155679, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.99373180254821, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.77339506654047, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295155679 }, { "Sample": "659_bQZ-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.10827944196947, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.858591011559, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295155679, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.10827944196947, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.858591011559, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295155679 }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 370869163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591384920, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.004932, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.487718, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 302955668, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.947428, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.976419, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.042944, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.023581, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 287028540, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 145324495, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13010268, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3509690, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 622.161437, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 239, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.714797, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.615107, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97491, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 165.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 151, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.68, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.33, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 286, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 801.844813, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.490136, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.9736, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 92.50978559558136, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.58, "STAR_mqc-generalstats-star-uniquely_mapped": 285588384, "fastp_mqc-generalstats-fastp-pct_duplication": 36.2785, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974041, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78991503335, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591384920, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.547694, "fastp_mqc-generalstats-fastp-pct_surviving": 98.56415333333334, "fastp_mqc-generalstats-fastp-pct_adapter": 42.2137825, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 165.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.48412096811667, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 291210120, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.85373802004902, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 454856629, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.36007842377282, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 454856629, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.24794329501267, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.07950479697723, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295692460, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.24794329501267, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.07950479697723, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295692460 }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.00490732018683, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.16844278680625, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295692460, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.00490732018683, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.16844278680625, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295692460 }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 189032919, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589227876, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.00529, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.636652, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 214094561, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.935481, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.970907, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.04996, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.029093, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 200281438, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 101338884, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10696203, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3036578, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 420.014797, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 150, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.679334, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.559365, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975105, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 164.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.78, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.75, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.56, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.11, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 289, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 787.054623, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.640038, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.9472, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 92.28090810351259, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.48, "STAR_mqc-generalstats-star-uniquely_mapped": 284253416, "fastp_mqc-generalstats-fastp-pct_duplication": 49.574600000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974174, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78202005484, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589227876, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.551828, "fastp_mqc-generalstats-fastp-pct_surviving": 98.204646, "fastp_mqc-generalstats-fastp-pct_adapter": 43.006330166666665, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 164.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.48354900303461, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290146262, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.689798322538, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 484498677, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.39368522811846, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 484498677, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.84295415129031, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.17981472078216, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294613938, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.84295415129031, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.17981472078216, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294613938 }, { "Sample": "659_bTo-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.16778174506759, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.28435108185548, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294613938, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.16778174506759, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.28435108185548, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294613938 }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 407394333, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 312959954, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006282, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.349485, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 203584985, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.949905, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.97879, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.040439, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.02121, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 193386305, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 97954843, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 8232716, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2122647, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 430.249528, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 155, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.673097, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.558066, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975298, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 170.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 154, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.51, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.74, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.94, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 266, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 812.886954, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.351695, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 98.2098, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.38847351314176, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.36, "STAR_mqc-generalstats-star-uniquely_mapped": 146087529, "fastp_mqc-generalstats-fastp-pct_duplication": 25.072400000000002, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974307, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 41992751807, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 312959954, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.533943, "fastp_mqc-generalstats-fastp-pct_surviving": 98.53795484469849, "fastp_mqc-generalstats-fastp-pct_adapter": 40.69175600291005, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 170.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.45111045741015, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 154056275, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.69554778190856, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 158801730, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.32173974552451, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 158801730, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.70795721214346, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.6700330931158, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 156479977, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 80.70795721214346, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 52, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.6700330931158, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 156479977 }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.46951508637831, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.75334397575992, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 156479977, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 81.46951508637831, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.75334397575992, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 156479977 }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 321306908, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591729018, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005923, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.510009, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 289941721, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.94254, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.975509, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.045373, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.024491, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 273281564, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 138515622, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13155477, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3477595, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 603.700653, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 229, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.701739, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.599497, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974753, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 169.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 154, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.48, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.65, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.95, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 269, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 820.444198, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.513048, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 98.1996, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.77868874937123, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.54, "STAR_mqc-generalstats-star-uniquely_mapped": 276756604, "fastp_mqc-generalstats-fastp-pct_duplication": 38.205600000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973843, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79442730619, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591729018, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.534875, "fastp_mqc-generalstats-fastp-pct_surviving": 98.621503, "fastp_mqc-generalstats-fastp-pct_adapter": 40.64577416666666, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 169.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.4763660855314, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 291356617, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.81581649566175, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 310024657, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.23678776354824, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 310024657, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.65608812195072, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.8134212643937, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295864509, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.65608812195072, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.8134212643937, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295864509 }, { "Sample": "659_bUW-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.14284793071013, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.89713562095412, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295864509, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.14284793071013, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.89713562095412, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295864509 }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 248353122, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590660126, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005961, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.59458, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 239465725, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.930242, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.965919, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055055, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.034081, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 222761030, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 112928509, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13183726, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3984557, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 476.644566, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 209, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.730819, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.616448, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97474, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 166.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.36, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 288, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 750.134551, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.598145, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3013, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 92.20891632331326, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.5, "STAR_mqc-generalstats-star-uniquely_mapped": 284981550, "fastp_mqc-generalstats-fastp-pct_duplication": 45.1092, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97379, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78722008968, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590660126, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.555199, "fastp_mqc-generalstats-fastp-pct_surviving": 98.44335433333333, "fastp_mqc-generalstats-fastp-pct_adapter": 42.85477316666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 166.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.2379284563387, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290126136, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.57246774125232, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 331855698, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.90491391779801, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 331855698, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.89329548165983, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.81235746731278, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295330063, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.89329548165983, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.81235746731278, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295330063 }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.45190407962204, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.90559073899632, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295330063, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.45190407962204, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.90559073899632, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295330063 }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 136397683, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590746412, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005899, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.708293, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 172324792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.914443, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.958856, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.065337, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.041144, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 157581142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 80055474, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11259102, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3435135, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 341.18787, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 141, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.699548, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.560755, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974008, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 175.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 161, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.36, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.32, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 342, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 865.542011, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.712496, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2016, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 92.39024057772966, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.57, "STAR_mqc-generalstats-star-uniquely_mapped": 285254927, "fastp_mqc-generalstats-fastp-pct_duplication": 55.964400000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973034, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 80400064132, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590746412, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.555548, "fastp_mqc-generalstats-fastp-pct_surviving": 98.45773533333333, "fastp_mqc-generalstats-fastp-pct_adapter": 36.85211683333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 175.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.15544169568312, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289924875, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.52771181352472, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 388390796, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.48628950687956, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 388390796, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.89512767665315, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.82811397591695, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295373206, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.89512767665315, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.82811397591695, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295373206 }, { "Sample": "659_bhK-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.1384656638406, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.90109208822415, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295373206, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.1384656638406, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.90109208822415, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295373206 }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 297227450, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590980670, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006671, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.517888, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 284919117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.932022, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962966, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.054142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037035, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 265550775, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 134215858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15425960, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5161782, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 526.490156, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 270, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.762264, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.657465, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974498, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 150.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 139, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.59, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.39, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.88, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 197, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 512.095112, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.521366, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2677, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.14652670157523, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.75, "STAR_mqc-generalstats-star-uniquely_mapped": 282945193, "fastp_mqc-generalstats-fastp-pct_duplication": 37.5766, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973552, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76037204592, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590980670, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.537109, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49677833333334, "fastp_mqc-generalstats-fastp-pct_adapter": 52.872425, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 150.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.07991723316432, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289816676, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.59062459466566, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 315604483, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.88263200474796, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 315604483, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.27372669816734, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.08977852355136, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295490335, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.27372669816734, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.08977852355136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295490335 }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.78313784498769, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.21331010708016, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295490335, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.78313784498769, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.21331010708016, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295490335 }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 179416459, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 447523764, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006406, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.571644, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 191699362, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.927577, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.960297, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.057467, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.039703, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 177815969, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 89879896, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11016359, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3716047, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 353.074862, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 174, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.728934, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.599089, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97601, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 152.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 141, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.06, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.58, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.35, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.87, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 206, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 549.884183, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.57533, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.25059999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.31086527185337, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.82, "STAR_mqc-generalstats-star-uniquely_mapped": 214418117, "fastp_mqc-generalstats-fastp-pct_duplication": 41.742200000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.975142, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 58194435620, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 447523764, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.534483, "fastp_mqc-generalstats-fastp-pct_surviving": 98.53350605321386, "fastp_mqc-generalstats-fastp-pct_adapter": 51.08837898091381, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 152.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.09406188315846, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 219497119, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.65258542732252, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227092175, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.37703509401737, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227092175, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.66161901877808, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.2851930160294, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 223761882, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.66161901877808, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.2851930160294, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 223761882 }, { "Sample": "659_buD-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.47563286076614, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.40419851760095, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 223761882, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.47563286076614, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.40419851760095, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 223761882 }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 292363696, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591453148, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.00548, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.533066, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 276169830, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.933022, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962098, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055241, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037902, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 257672492, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 130256862, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15255938, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5131451, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 516.301702, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 205, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.6915, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.592891, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974866, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 150.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 140, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.69, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.26, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 194, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 468.326323, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.536003, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.9839, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.42633462201458, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.23, "STAR_mqc-generalstats-star-uniquely_mapped": 284583308, "fastp_mqc-generalstats-fastp-pct_duplication": 37.9576, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97388, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76550454440, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591453148, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.540415, "fastp_mqc-generalstats-fastp-pct_surviving": 98.57552466666667, "fastp_mqc-generalstats-fastp-pct_adapter": 51.2423965, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 150.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.99739742022643, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289804346, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.28343950916583, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 384362610, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.63386170391533, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 384362610, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.38433901920129, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.83320387365663, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295726574, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.38433901920129, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.83320387365663, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295726574 }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.90610404516241, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.9514544472422, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295726574, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.90610404516241, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.9514544472422, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295726574 }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 168233575, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591101856, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005644, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.674081, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 192651298, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.915877, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.952264, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.066807, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.047736, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 176444879, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 89212001, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12870521, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4472075, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 349.916221, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 130, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.658499, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.539563, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974526, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 152.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 141, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.58, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.42, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.87, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 206, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 501.68798400000003, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.677907, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.00720000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.38230927117411, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.25, "STAR_mqc-generalstats-star-uniquely_mapped": 284470413, "fastp_mqc-generalstats-fastp-pct_duplication": 49.9283, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973541, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77057557730, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591101856, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546379, "fastp_mqc-generalstats-fastp-pct_surviving": 98.516976, "fastp_mqc-generalstats-fastp-pct_adapter": 49.86518033333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 152.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.00289444531874, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289648464, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.95465805818326, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 325084319, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.2064712688029, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 325084319, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.38415103915919, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.84091606709487, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295550928, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.38415103915919, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.84091606709487, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295550928 }, { "Sample": "659_bua-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.78634142525223, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.95721194622675, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295550928, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.78634142525223, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.95721194622675, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295550928 }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 405212395, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591386466, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006124, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.467382, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 314983309, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.936162, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.967092, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.052341, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.032908, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 294875278, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 149417923, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 16486596, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5084312, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 622.212264, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 306, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.753804, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.654974, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975184, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0.16, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 162.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.45, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.17, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.67, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 232, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 608.716454, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.470261, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.214, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.39082856331864, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.73, "STAR_mqc-generalstats-star-uniquely_mapped": 283056288, "fastp_mqc-generalstats-fastp-pct_duplication": 34.224199999999996, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97427, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77982574684, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591386466, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.539414, "fastp_mqc-generalstats-fastp-pct_surviving": 98.56441099999999, "fastp_mqc-generalstats-fastp-pct_adapter": 45.369647666666665, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 162.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.79918331780017, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289185567, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.04170170896488, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 348090083, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.41309710454992, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 348090083, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.05261827123434, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.2905273824782, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295693233, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.05261827123434, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.2905273824782, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295693233 }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.53006935562824, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.39012685826327, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295693233, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.53006935562824, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.39012685826327, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295693233 }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 281529652, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 579786172, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006149, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.529302, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 272903925, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.931121, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.964996, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055816, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.035004, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 254106575, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 128856226, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15232534, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4674033, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 540.828739, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 261, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.742307, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.638019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975271, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0.13, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 167, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.96, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.44, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 245, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 650.203741, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.532577, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1613, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.38124364805084, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.74, "STAR_mqc-generalstats-star-uniquely_mapped": 277530262, "fastp_mqc-generalstats-fastp-pct_duplication": 40.0715, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97433, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77331014303, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 579786172, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.539659, "fastp_mqc-generalstats-fastp-pct_surviving": 98.47661334416432, "fastp_mqc-generalstats-fastp-pct_adapter": 42.653926498720125, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 167, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.75984308918633, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 283399026, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.48602768677218, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294377595, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.94745363352506, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294377595, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.56563401351556, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.8394328693993, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 289893086, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.56563401351556, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.8394328693993, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 289893086 }, { "Sample": "659_c95-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.17436673519023, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.93335145288702, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 289893086, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.17436673519023, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.93335145288702, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 289893086 }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 264556305, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 534805094, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007589, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.522796, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 255211176, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.928717, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.958508, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055379, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.041492, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 237019062, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 119425222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14133255, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5169679, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 440.809404, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 191, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.724054, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.602302, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974933, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0.03, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 140.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 132, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.05, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 156, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 317.972842, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.526794, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2148, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.88527276954417, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.31, "STAR_mqc-generalstats-star-uniquely_mapped": 254872531, "fastp_mqc-generalstats-fastp-pct_duplication": 35.911, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973831, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 67113581197, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 534805094, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.550423, "fastp_mqc-generalstats-fastp-pct_surviving": 98.48155774537645, "fastp_mqc-generalstats-fastp-pct_adapter": 60.59510799915463, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 140.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.92594645704702, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 261856475, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.46284785848914, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 271525505, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.89464897698323, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 271525505, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.5443021497323, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.7793510508335, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 267402547, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.5443021497323, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.7793510508335, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 267402547 }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.09135056685227, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.93414527199698, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 267402547, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.09135056685227, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.93414527199698, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 267402547 }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 168421019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589788690, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.669708, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 194802467, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.908315, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.946636, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.068092, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.053364, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 176942032, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 89146541, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13264557, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5025438, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 322.669121, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 133, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.692048, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.549376, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.976071, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 140.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 132, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.18, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.68, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.15, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 160, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 331.937748, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.674968, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1518, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.86286843723103, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.3, "STAR_mqc-generalstats-star-uniquely_mapped": 281022721, "fastp_mqc-generalstats-fastp-pct_duplication": 48.5572, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974948, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 74017738217, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589788690, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553412, "fastp_mqc-generalstats-fastp-pct_surviving": 98.298115, "fastp_mqc-generalstats-fastp-pct_adapter": 60.023452666666664, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 140.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.82773725281169, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288488465, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.09735497253611, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 337660048, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.02413493020491, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 337660048, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.2363023406912, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.63719149310916, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294894345, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.2363023406912, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.63719149310916, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294894345 }, { "Sample": "659_cAd-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.57243949022894, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 128.79684566009564, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294894345, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.57243949022894, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 128.79684566009564, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294894345 }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 299663468, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 585007414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005202, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.521133, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 280140651, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.936949, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.966859, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.052187, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.033141, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 262477458, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 132859029, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14619710, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4554000, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 555.642893, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 235, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.722557, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.619345, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97358, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 163.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 150, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.91, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.81, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 226, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 616.916836, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.523859, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3521, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.78818955187069, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.44, "STAR_mqc-generalstats-star-uniquely_mapped": 282078903, "fastp_mqc-generalstats-fastp-pct_duplication": 37.696000000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972603, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77598711507, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 585007414, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.541454, "fastp_mqc-generalstats-fastp-pct_surviving": 98.41805661848046, "fastp_mqc-generalstats-fastp-pct_adapter": 44.219165021897474, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 163.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.13194435857184, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 287039575, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.10700909789516, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 297205327, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.49329462379241, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 297205327, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.14942058386255, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.32828341214835, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 292503707, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.14942058386255, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.32828341214835, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 292503707 }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.66578417427763, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.4231760864487, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 292503707, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.66578417427763, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.4231760864487, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 292503707 }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 194899623, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590849882, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005179, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.628579, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 219454165, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.926415, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.960283, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.059641, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.039717, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 203305689, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 102927009, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13088437, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4257081, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 422.48377, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 170, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.698272, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.581334, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975022, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 162.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 148, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.59, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.4, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.9, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 228, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 605.158733, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.631851, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3347, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.74862865987369, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.44, "STAR_mqc-generalstats-star-uniquely_mapped": 284909229, "fastp_mqc-generalstats-fastp-pct_duplication": 47.4892, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974098, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78212614510, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590849882, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546939, "fastp_mqc-generalstats-fastp-pct_surviving": 98.47498033333333, "fastp_mqc-generalstats-fastp-pct_adapter": 44.53121733333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 162.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.09742163915674, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289804250, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.36773585919305, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 370069558, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.69650372775905, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 370069558, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.85990848772447, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.8390662181769, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295424941, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.85990848772447, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.8390662181769, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295424941 }, { "Sample": "659_cIX-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.44632688231972, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.93501553411497, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295424941, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.44632688231972, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.93501553411497, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295424941 }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 148045895, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 477824582, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006969, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.668065, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 158606692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.910123, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.942385, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.068881, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.057615, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 144351545, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 72522803, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10925019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4433840, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 243.203375, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 115, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.687395, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.528136, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974436, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 128.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 122, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.99, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.24, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.96, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 147, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 298.043762, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.672754, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.27799999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.37007426915231, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.52, "STAR_mqc-generalstats-star-uniquely_mapped": 228216617, "fastp_mqc-generalstats-fastp-pct_duplication": 43.940200000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973302, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 57419811412, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 477824582, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.547649, "fastp_mqc-generalstats-fastp-pct_surviving": 98.45425621382633, "fastp_mqc-generalstats-fastp-pct_adapter": 70.15487673178423, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 128.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.07503834116261, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 234313321, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.34791368540702, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 242663243, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.32228893480949, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 242663243, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.39056748859498, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 123.36427587143267, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 238912291, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.39056748859498, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 123.36427587143267, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 238912291 }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.48293313554055, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 123.55339293113221, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 238912291, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.48293313554055, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 123.55339293113221, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 238912291 }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 111403143, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 567211638, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006759, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.782022, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 123639576, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.884932, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.927321, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.084058, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.072679, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 109412618, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 54950163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10392931, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4306725, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 182.870677, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 82, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.651921, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.457747, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975592, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 129.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 123, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.07, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.67, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.54, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.06, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 156, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 329.360022, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.787344, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.38560000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.57621169635462, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.59, "STAR_mqc-generalstats-star-uniquely_mapped": 271099394, "fastp_mqc-generalstats-fastp-pct_duplication": 55.3494, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974552, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 68756557335, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 567211638, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.550838, "fastp_mqc-generalstats-fastp-pct_surviving": 98.4455530079531, "fastp_mqc-generalstats-fastp-pct_adapter": 68.5315322221148, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 129.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.13558268351328, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 278318223, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.2991190336758, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 288083931, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.18547556846723, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 288083931, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.35715530816807, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.28881386245463, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 283605819, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.35715530816807, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.28881386245463, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 283605819 }, { "Sample": "659_cRB-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.39540916964606, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.46490180090416, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 283605819, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.39540916964606, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.46490180090416, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 283605819 }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 279883847, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591216258, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006009, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.556225, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 262367007, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.934767, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.967044, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.051692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.032956, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 245252008, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 124106142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13562222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4229390, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 523.664269, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 253, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.753677, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.645518, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974947, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 159.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 146, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.83, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.49, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.99, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 286, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 690.061505, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.559588, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.8291, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.348954444837, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.24, "STAR_mqc-generalstats-star-uniquely_mapped": 284486305, "fastp_mqc-generalstats-fastp-pct_duplication": 41.3108, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974017, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78325641837, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591216258, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.557503, "fastp_mqc-generalstats-fastp-pct_surviving": 98.53604299999999, "fastp_mqc-generalstats-fastp-pct_adapter": 44.58041766666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 159.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.22387698952623, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290357765, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.971949863848, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 440006046, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.43312412270639, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 440006046, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.40385447891826, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.9619323831247, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295608129, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.40385447891826, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.9619323831247, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295608129 }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.22319070917531, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.05890015967728, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295608129, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.22319070917531, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.05890015967728, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295608129 }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 166634867, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590334908, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006266, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.662604, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 199176837, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.92334, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.961807, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.058089, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.038193, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 183907985, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 93062627, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11570002, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3695460, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 388.847728, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 178, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.725699, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.599479, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973672, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 162, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.87, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.24, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.88, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 312, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 721.315992, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.666782, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.85740000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.29480406541414, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.21, "STAR_mqc-generalstats-star-uniquely_mapped": 283979684, "fastp_mqc-generalstats-fastp-pct_duplication": 50.560300000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972715, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78366718311, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590334908, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.56237, "fastp_mqc-generalstats-fastp-pct_surviving": 98.38915133333333, "fastp_mqc-generalstats-fastp-pct_adapter": 43.68399533333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 162, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.2026619371118, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289862297, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.44216454918325, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 483394385, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.44702149564375, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 483394385, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.4350383173635, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.4183398011083, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295167454, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.4350383173635, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.4183398011083, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295167454 }, { "Sample": "659_cRa-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.98286687761146, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.51603594480304, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295167454, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.98286687761146, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.51603594480304, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295167454 }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 334791242, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591121784, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006682, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.49759, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 296985217, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.93674, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.967015, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.04996, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.032985, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 278198035, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 140564017, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14837374, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4794593, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 561.007414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 293, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.784385, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.679818, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974284, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 152, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 139, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.89, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.52, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.79, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.78, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 207, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 551.443993, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.500938, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6247, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.37265278733535, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.75, "STAR_mqc-generalstats-star-uniquely_mapped": 282986257, "fastp_mqc-generalstats-fastp-pct_duplication": 35.471599999999995, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973311, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76208007866, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591121784, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.545103, "fastp_mqc-generalstats-fastp-pct_surviving": 98.52029733333333, "fastp_mqc-generalstats-fastp-pct_adapter": 51.90854350000001, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 152, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.00690207688235, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289670074, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.9388622742832, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 391105525, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.23138384838565, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 391105525, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.04691904830906, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.38636496265548, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295560892, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.04691904830906, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.38636496265548, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295560892 }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.55684565669264, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.51345839083473, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295560892, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.55684565669264, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.51345839083473, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295560892 }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 196360611, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591122682, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007196, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.616835, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 226497613, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.926368, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.964386, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.054852, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.035614, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 209820196, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 106213825, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12423812, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3922422, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 436.359177, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 218, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.763033, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.641693, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975224, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 164.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.87, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.82, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.83, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 264, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 732.46439, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.621306, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.5982, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.89904247012332, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.85, "STAR_mqc-generalstats-star-uniquely_mapped": 283299502, "fastp_mqc-generalstats-fastp-pct_duplication": 47.944199999999995, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974266, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79292255981, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591122682, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.545307, "fastp_mqc-generalstats-fastp-pct_surviving": 98.520447, "fastp_mqc-generalstats-fastp-pct_adapter": 42.339319833333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 164.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.822761942334, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289126267, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.90235246399905, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 384196562, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.82995981020284, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 384196562, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.12184860683608, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.6339570877776, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295561341, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.12184860683608, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.6339570877776, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295561341 }, { "Sample": "659_cTi-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.44193887786416, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.7160562077704, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295561341, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.44193887786416, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.7160562077704, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295561341 }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 324761133, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590880390, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006562, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.490907, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 300812838, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.934402, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.968142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.052709, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.031858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 281080174, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 142501900, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15855460, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4689163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 617.067117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 287, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.753743, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.650014, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974423, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 172.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 156, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.13, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 234, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 580.588411, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.49415, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3239, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.62172780535758, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.26, "STAR_mqc-generalstats-star-uniquely_mapped": 281425031, "fastp_mqc-generalstats-fastp-pct_duplication": 37.4535, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973406, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79231829493, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590880390, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.558247, "fastp_mqc-generalstats-fastp-pct_surviving": 98.48006500000001, "fastp_mqc-generalstats-fastp-pct_adapter": 39.667799333333335, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 172.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.96195470287988, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289418990, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.57333225005038, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 327172275, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.80259179826942, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 327172275, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.00950381220382, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.70207125675637, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295440195, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.00950381220382, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.70207125675637, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295440195 }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.37568445217768, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.7958363282288, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295440195, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.37568445217768, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.7958363282288, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295440195 }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 187449459, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590529712, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006584, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.618228, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 225447751, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.921091, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962105, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.061663, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037895, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 207657880, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 105467068, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13901672, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4154051, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 460.759788, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 202, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.726445, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.608022, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 178.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 162, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.21, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.51, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.99, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.83, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 258, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 649.309348, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.622325, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2381, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.76714468772428, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.31, "STAR_mqc-generalstats-star-uniquely_mapped": 281406187, "fastp_mqc-generalstats-fastp-pct_duplication": 49.228, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973191, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 80341033832, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590529712, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.563305, "fastp_mqc-generalstats-fastp-pct_surviving": 98.42161866666666, "fastp_mqc-generalstats-fastp-pct_adapter": 35.38923366666666, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 178.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.81576646561689, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288815582, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.89568194988551, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 412352249, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.04867809787768, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 412352249, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.77284494371992, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.75170243085077, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295264856, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.77284494371992, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.75170243085077, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295264856 }, { "Sample": "659_cVw-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.33407369820785, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.83103711469136, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295264856, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.33407369820785, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.83103711469136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295264856 }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 203053246, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 588173086, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007061, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.620766, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 223055005, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.91515, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.9548, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.06623, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.0452, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 204128720, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 103311364, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14772966, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4890718, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 408.476117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 152, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.710065, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.570787, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.972109, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 157.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.15, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.74, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 193, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 379.724106, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.625181, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.4836, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.1424683785849, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.87, "STAR_mqc-generalstats-star-uniquely_mapped": 279001503, "fastp_mqc-generalstats-fastp-pct_duplication": 46.021699999999996, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.970887, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76554669602, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 588173086, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.593999, "fastp_mqc-generalstats-fastp-pct_surviving": 98.02884766666666, "fastp_mqc-generalstats-fastp-pct_adapter": 47.75638716666666, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 157.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.43827720808021, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 286552861, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.72499768150406, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 371930849, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.49585177460573, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 371930849, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.1794401164597, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.97937134784164, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294086543, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.1794401164597, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.97937134784164, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294086543 }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.6093120366545, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.12781392380813, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294086543, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.6093120366545, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.12781392380813, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294086543 }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 150763487, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 559540888, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007045, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.697277, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 169385768, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.90441, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.950412, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.072318, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.049588, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 153194173, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 77693542, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 12249717, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4053646, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 312.553747, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 110, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.679101, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.517808, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973371, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 167.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 155, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.17, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.48, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.79, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 217, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 434.634143, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.702224, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.44749999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.60417418367527, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95, "STAR_mqc-generalstats-star-uniquely_mapped": 265791637, "fastp_mqc-generalstats-fastp-pct_duplication": 55.287600000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.9722, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75085911246, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 559540888, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.598301, "fastp_mqc-generalstats-fastp-pct_surviving": 98.22903585231232, "fastp_mqc-generalstats-fastp-pct_adapter": 40.650218165756044, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 167.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.18904974822858, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 271906236, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.57631750573776, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 284814405, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.40586589253905, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 284814405, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.63412058540924, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.97187705431816, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 279770444, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.63412058540924, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 59, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.97187705431816, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 279770444 }, { "Sample": "659_cWx-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.86290729371423, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.07406991497643, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 279770444, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.86290729371423, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.07406991497643, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 279770444 }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 309136353, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590927154, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.004885, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.50853, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 290422997, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.941943, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.971285, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.048117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.028715, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 273562039, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 138483577, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13974170, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4094092, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 580.106167, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 247, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.729343, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.624846, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974807, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 163.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.95, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.64, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.93, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.92, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 244, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 659.384902, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.511026, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.66890000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.64016457232434, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.32, "STAR_mqc-generalstats-star-uniquely_mapped": 284593221, "fastp_mqc-generalstats-fastp-pct_duplication": 38.053599999999996, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973841, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78631142281, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590927154, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.554895, "fastp_mqc-generalstats-fastp-pct_surviving": 98.487859, "fastp_mqc-generalstats-fastp-pct_adapter": 43.93142866666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 163.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.22864325507032, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290229863, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.61915226345519, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 379513854, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.77421176318092, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 379513854, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.00976638052384, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.58246625776144, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295463577, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.00976638052384, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.58246625776144, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295463577 }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.45506284773039, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.681288556931, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295463577, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.45506284773039, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.681288556931, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295463577 }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 164194879, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 588716550, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005299, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.68051, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 188088891, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.923582, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.961161, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.059832, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.038839, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 173715580, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 87860795, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11253770, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3550298, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 352.204847, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 139, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.682842, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.552036, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973566, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 161.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 146, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.07, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.29, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 239, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 629.45609, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.684135, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6419, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.2191312335785, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.17, "STAR_mqc-generalstats-star-uniquely_mapped": 283093186, "fastp_mqc-generalstats-fastp-pct_duplication": 51.7133, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972488, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77396008035, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 588716550, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.558522, "fastp_mqc-generalstats-fastp-pct_surviving": 98.119425, "fastp_mqc-generalstats-fastp-pct_adapter": 45.462746833333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 161.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.20744397282529, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289081738, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.77439461189024, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 425582300, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.36701281525929, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 425582300, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.50580956666396, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.11875125644082, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294358275, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.50580956666396, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.11875125644082, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294358275 }, { "Sample": "659_cfy-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.76965032818195, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.23862019846393, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294358275, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.76965032818195, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.23862019846393, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294358275 }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 355296639, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590628272, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006703, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.47762, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 308532615, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.932722, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.966658, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.054447, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.033342, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 287775082, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 146005068, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 16798738, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5036081, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 609.38091, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 299, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.780012, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.66903, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974658, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 165.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.82, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.41, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.59, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 219, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 525.105285, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.480843, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.60079999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.26340051427715, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.79, "STAR_mqc-generalstats-star-uniquely_mapped": 282887174, "fastp_mqc-generalstats-fastp-pct_duplication": 36.7562, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973651, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78785640346, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590628272, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.562477, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43804533333333, "fastp_mqc-generalstats-fastp-pct_adapter": 42.16985233333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 165.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.60444721819887, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288239730, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.71115091291998, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 379870111, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.95284092212503, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 379870111, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.98330157297198, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.94955323439038, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295314136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.98330157297198, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.94955323439038, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295314136 }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.59815733211582, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.0441027448818, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295314136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.59815733211582, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.0441027448818, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295314136 }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 240163170, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590612628, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006527, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.561124, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 259205490, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.923418, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962069, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.06171, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037931, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 239355136, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 121693116, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15995656, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4797873, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 515.82892, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 251, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.766485, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.647123, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974857, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 172.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 158, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.81, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.4, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 238, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 592.605677, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.564811, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.4155, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.54857842083572, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.91, "STAR_mqc-generalstats-star-uniquely_mapped": 283218650, "fastp_mqc-generalstats-fastp-pct_duplication": 44.0869, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973877, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 80000201992, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590612628, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.559866, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43543799999999, "fastp_mqc-generalstats-fastp-pct_adapter": 38.229977500000004, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 172.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.46310300700173, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 287814697, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.46473217075184, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 345246340, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.67906427477239, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 345246340, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.39253610281796, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.03889034015032, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295306314, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.39253610281796, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.03889034015032, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295306314 }, { "Sample": "659_ciJ-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.9537100356255, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.12160076265758, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295306314, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.9537100356255, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.12160076265758, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295306314 }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 211594042, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590996452, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006363, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.627325, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 220249688, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.922646, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.953032, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.06028, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.046968, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 203212584, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 102297486, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13276562, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5041480, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 359.117757, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 161, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.704976, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.578875, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97281, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 136.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 129, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.97, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.95, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 151, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 331.315535, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.631342, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.613, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.72335974998202, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.2, "STAR_mqc-generalstats-star-uniquely_mapped": 281324917, "fastp_mqc-generalstats-fastp-pct_duplication": 42.8594, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971668, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 73062119593, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590996452, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.530287, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49940866666667, "fastp_mqc-generalstats-fastp-pct_adapter": 64.82353499999999, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 136.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.1172617936461, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289934768, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.09233751708803, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 304962074, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.12603804317996, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 304962074, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.01823568654068, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.14163045093882, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295498226, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.01823568654068, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 52, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.14163045093882, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295498226 }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.19593328236544, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.30345371684228, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295498226, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.19593328236544, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.30345371684228, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295498226 }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 133743938, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590606900, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006256, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.766966, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 137631396, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.893316, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.933504, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.07984, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.066496, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 122948273, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 61835974, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10988424, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4404716, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 208.306556, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 86, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.646351, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.470812, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973774, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 132.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 126, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.88, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.74, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 5.4, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 143, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 292.030914, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.771794, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.62429999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.35027860634142, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.09, "STAR_mqc-generalstats-star-uniquely_mapped": 280796665, "fastp_mqc-generalstats-fastp-pct_duplication": 51.858000000000004, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972684, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 71372906403, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590606900, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.539488, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43448333333333, "fastp_mqc-generalstats-fastp-pct_adapter": 67.6794725, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 132.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.09722609065354, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289684493, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.75620073414876, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 326972626, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.54313221285757, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 326972626, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.22857178453593, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.14312917779999, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295303450, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.22857178453593, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.14312917779999, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295303450 }, { "Sample": "659_ciZ-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.21380906471364, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.32356210535299, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295303450, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.21380906471364, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.32356210535299, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295303450 }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 233990666, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 550091604, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006295, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.550979, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 247002771, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.921946, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.954142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.064035, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.045858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 227723128, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 115225578, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15816702, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5537956, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 446.799081, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 234, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.754272, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.637222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975035, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 155.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.92, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.37, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 173, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 323.762014, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.554469, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.89229999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.48656392194188, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.63, "STAR_mqc-generalstats-star-uniquely_mapped": 263027568, "fastp_mqc-generalstats-fastp-pct_duplication": 40.4391, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973969, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 71796078728, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 550091604, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.552307, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43180901104662, "fastp_mqc-generalstats-fastp-pct_adapter": 49.55876342180072, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 155.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.38979437322952, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 267866541, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.2900978658433, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 279427763, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.82848820946202, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 279427763, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.32667591390151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 133.94068012715934, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 275045802, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 81.32667591390151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 133.94068012715934, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 275045802 }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.03363164345001, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.05542330000733, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 275045802, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.03363164345001, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.05542330000733, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 275045802 }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 142680172, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 420786928, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006148, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.631352, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 155122232, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.911245, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.947921, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.072078, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.052079, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 141354299, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 71585979, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11180911, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3932966, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 279.627222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.711088, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.564046, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974341, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 161.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 150, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.89, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.93, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.54, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 185, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 358.476163, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.635258, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.7762, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.63040269500515, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.7, "STAR_mqc-generalstats-star-uniquely_mapped": 201348608, "fastp_mqc-generalstats-fastp-pct_duplication": 48.5896, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973286, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 55927814614, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 420786928, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.551033, "fastp_mqc-generalstats-fastp-pct_surviving": 98.41498951758926, "fastp_mqc-generalstats-fastp-pct_adapter": 44.94133320809668, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 161.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.32004317396475, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 204755010, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.16221625432726, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 213781930, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.60269408703098, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 213781930, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.2009200507479, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.50224168560675, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 210393464, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.2009200507479, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.50224168560675, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 210393464 }, { "Sample": "659_d01-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.76071509843585, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.60529504376618, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 210393464, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.76071509843585, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.60529504376618, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 210393464 }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 325524298, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591685756, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006535, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.495994, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 298213228, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.928254, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.95716, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.05878, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.04284, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 276817668, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 139835325, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 17528903, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 6258707, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 555.728469, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 278, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.75518, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.648834, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975495, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 154.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.22, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.84, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 187, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 454.681438, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.499257, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.0752, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.71505656003735, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.35, "STAR_mqc-generalstats-star-uniquely_mapped": 282077309, "fastp_mqc-generalstats-fastp-pct_duplication": 38.1419, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974542, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77433459794, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591685756, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.528492, "fastp_mqc-generalstats-fastp-pct_surviving": 98.61429266666667, "fastp_mqc-generalstats-fastp-pct_adapter": 49.78005733333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 154.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.83946463636012, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289451088, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.13980228208996, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 324361695, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.83256207842012, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 324361695, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.5687714767868, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.22820297536452, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295842878, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.5687714767868, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 52, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.22820297536452, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295842878 }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.33736663902116, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.33345252610746, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295842878, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.33736663902116, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.33345252610746, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295842878 }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 183489136, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 514089484, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006669, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.594653, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 208384394, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.916783, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.949905, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.066765, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.050095, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 191043305, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 96527234, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13912806, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5090510, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 379.045502, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 181, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.720682, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.595197, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975279, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 156.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.33, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.42, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.2, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 188, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 448.494593, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.598646, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.0453, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.65575207516899, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.35, "STAR_mqc-generalstats-star-uniquely_mapped": 245092177, "fastp_mqc-generalstats-fastp-pct_duplication": 45.504, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974281, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 67152923104, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 514089484, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.533218, "fastp_mqc-generalstats-fastp-pct_surviving": 98.42102038783078, "fastp_mqc-generalstats-fastp-pct_adapter": 49.937510084484146, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 156.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.8030147763147, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 251397507, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.81523825369256, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 261168540, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.32029054559766, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 261168540, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.86424438191241, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.01233830723524, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 257044742, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.86424438191241, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 52, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.01233830723524, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 257044742 }, { "Sample": "659_dES-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.58577513444104, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.12017557239122, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 257044742, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.58577513444104, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.12017557239122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 257044742 }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 291400994, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590597348, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006131, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.516552, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 285523121, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.930459, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.963221, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.056858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.036779, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 265667720, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 134638059, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 16234328, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5140949, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 553.519207, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 287, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.760771, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.655392, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974864, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 164, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 150, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.05, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.65, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 216, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 527.225796, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.519739, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.69839999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.52784993632076, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.54, "STAR_mqc-generalstats-star-uniquely_mapped": 282138968, "fastp_mqc-generalstats-fastp-pct_duplication": 38.8048, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973772, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78297753149, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590597348, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.550862, "fastp_mqc-generalstats-fastp-pct_surviving": 98.43289133333334, "fastp_mqc-generalstats-fastp-pct_adapter": 44.15806633333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 164, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.6042398348189, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288224026, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.78774433235284, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 327628596, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.02379832405907, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 327628596, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.15037900511325, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.08457154128638, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295298674, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.15037900511325, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.08457154128638, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295298674 }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.5895772049796, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.1924568005341, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295298674, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.5895772049796, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.1924568005341, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295298674 }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 178442949, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590697900, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.639595, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 212890491, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.916316, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.955153, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.06652, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.044847, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 195075013, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 98934654, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14161384, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4645221, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 402.428369, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 198, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.732486, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.609383, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974578, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 163.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 150, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.64, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.51, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 5, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.81, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 220, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 526.466458, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.643576, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.636, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.20776115184051, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.43, "STAR_mqc-generalstats-star-uniquely_mapped": 281859593, "fastp_mqc-generalstats-fastp-pct_duplication": 49.2405, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973555, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78544536305, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590697900, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.556796, "fastp_mqc-generalstats-fastp-pct_surviving": 98.44965, "fastp_mqc-generalstats-fastp-pct_adapter": 43.215343499999996, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 163.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.34608976940666, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 287510654, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.51944299339172, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 346179532, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.54040443272784, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 346179532, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.48893614311437, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.52266696732798, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295348950, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.48893614311437, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.52266696732798, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295348950 }, { "Sample": "659_dc8-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.78631907449011, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.6269247816862, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295348950, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.78631907449011, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.6269247816862, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295348950 }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 46192447, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 180081228, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.009429, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.783297, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 39024059, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.813019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.861223, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.143469, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.138777, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 31727290, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 15895236, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 5598751, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2561351, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 46.973418, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 19, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.405464, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.120187, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974309, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 124.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 120, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.09, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.39, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 124, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 162.263436, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.790754, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.5866, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.96760094664587, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.01, "STAR_mqc-generalstats-star-uniquely_mapped": 84651561, "fastp_mqc-generalstats-fastp-pct_duplication": 53.4142, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972989, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 21071780887, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 180081228, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.54582, "fastp_mqc-generalstats-fastp-pct_surviving": 98.30878703910332, "fastp_mqc-generalstats-fastp-pct_adapter": 75.74959857064104, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 124.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.60032638160375, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 86979527, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.65750800125342, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 91589589, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.147821242866, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 91589589, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.65218411658265, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 120.14728579038788, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 90040614, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.65218411658265, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 120.14728579038788, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 90040614 }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.25029793203038, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 120.36244467413339, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 90040614, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.25029793203038, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 120.36244467413339, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 90040614 }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 26698224, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 120151114, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.00923, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.827891, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 20679065, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.765816, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.820233, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.180554, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.179767, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 15836368, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 7931071, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 3733691, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 1738217, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 23.175855, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 9, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.226596, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.03656, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974806, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 121.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 116, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.23, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.29, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.51, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 120, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 157.621461, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.835604, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.36630000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.76642286297853, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94, "STAR_mqc-generalstats-star-uniquely_mapped": 56473623, "fastp_mqc-generalstats-fastp-pct_duplication": 53.285700000000006, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97343, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 13759770365, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 120151114, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546864, "fastp_mqc-generalstats-fastp-pct_surviving": 97.81594926246237, "fastp_mqc-generalstats-fastp-pct_adapter": 77.63344633908297, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 121.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.29063614008606, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 57847136, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.46536294426372, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 61416934, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.31239985790086, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 61416934, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.41960103200796, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 117.52512626724376, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 117, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 60075557, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.41960103200796, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 117.52512626724376, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 117, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 60075557 }, { "Sample": "659_dcz-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.4386577339188, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 117.754702648866, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 117, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 60075557, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.4386577339188, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 117.754702648866, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 117, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 60075557 }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 236554736, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 527166558, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006328, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.548097, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 238227941, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.927641, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.955803, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.058355, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.044197, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 220989926, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 111414575, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13901882, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5151834, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 418.830639, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 183, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.710612, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.590255, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.976402, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 145.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 136, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.6, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.56, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.85, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.86, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 175, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 416.061948, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.551588, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3155, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.61891685330173, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.66, "STAR_mqc-generalstats-star-uniquely_mapped": 252138946, "fastp_mqc-generalstats-fastp-pct_duplication": 39.5981, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.975408, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 67379769268, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 527166558, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.534429, "fastp_mqc-generalstats-fastp-pct_surviving": 98.56183071532989, "fastp_mqc-generalstats-fastp-pct_adapter": 57.19218659030886, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 145.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.0315504004334, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 258394775, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.99512232696532, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 267429366, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.56365299487467, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 267429366, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.0392643061524, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.9659989699119, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 263583279, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.0392643061524, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.9659989699119, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 263583279 }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.70261601170392, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.09419752305305, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 263583279, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.70261601170392, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.09419752305305, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 263583279 }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 149003250, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589736474, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006481, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.693951, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 180488123, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.905139, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.940282, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.073685, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.059718, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 163366909, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 82192414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13299316, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5220124, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 289.964511, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 120, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.673511, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.530192, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974819, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 136.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 127, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.86, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 5.58, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 158, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 355.396697, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.698478, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2954, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.01805333532732, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.49, "STAR_mqc-generalstats-star-uniquely_mapped": 281571066, "fastp_mqc-generalstats-fastp-pct_duplication": 49.1477, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973766, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 72429498166, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589736474, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.537559, "fastp_mqc-generalstats-fastp-pct_surviving": 98.28941233333333, "fastp_mqc-generalstats-fastp-pct_adapter": 63.769084166666666, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 136.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.02005157985192, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289029998, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.50275139208233, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 336084304, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.30167847536353, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 336084304, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.72932698394548, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 126.02753031348033, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294868237, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.72932698394548, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 126.02753031348033, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294868237 }, { "Sample": "659_djb-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.87027294926317, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 126.21027466922455, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294868237, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.87027294926317, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 126.21027466922455, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294868237 }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 82623177, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 336261552, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007883, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.759823, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 80762386, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.85531, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.897263, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.111868, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.102738, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 69076845, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 34684624, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 9034736, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3971426, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 111.499847, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 49, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.591544, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.331256, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975706, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 131.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 126, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.12, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 133, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 185.486176, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.76586, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.6985, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.9603802685034, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.35, "STAR_mqc-generalstats-star-uniquely_mapped": 158636512, "fastp_mqc-generalstats-fastp-pct_duplication": 55.6413, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974387, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 41017382394, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 336261552, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.545124, "fastp_mqc-generalstats-fastp-pct_surviving": 98.40200804486109, "fastp_mqc-generalstats-fastp-pct_adapter": 68.35358766780433, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 131.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.01913527122483, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 163119025, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.99642389665495, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 170861123, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.64138809389308, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 170861123, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.03796347291922, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.0889142389969, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168130776, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.03796347291922, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.0889142389969, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 168130776 }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.84234640530732, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.27044978368505, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168130776, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.84234640530732, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.27044978368505, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 168130776 }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 52672785, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 266778546, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007963, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.833074, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 44532196, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.801369, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.855246, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.150926, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.144754, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 35686722, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 17896654, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 6721061, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3029074, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 55.961929, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 24, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.451615, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.152031, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 129.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 123, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.3, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.91, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 130, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 180.173985, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.839761, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 95.5719, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.14332277128545, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.19, "STAR_mqc-generalstats-star-uniquely_mapped": 125645333, "fastp_mqc-generalstats-fastp-pct_duplication": 58.5596, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972647, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 31951375388, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 266778546, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553601, "fastp_mqc-generalstats-fastp-pct_surviving": 98.056424910452, "fastp_mqc-generalstats-fastp-pct_adapter": 70.01405098373795, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 129.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.81776734775367, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 129144516, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.87638416586887, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 136033180, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.20798838805982, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 136033180, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.9071917184012, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 123.02854109565467, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 133389273, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.9071917184012, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 123.02854109565467, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 133389273 }, { "Sample": "659_dm4-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.52692734432307, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 123.22885323769626, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 133389273, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.52692734432307, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 123.22885323769626, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 133389273 }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 193305133, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 539858052, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.00789, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.596764, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 217690041, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.920405, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.95505, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.060028, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.04495, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 200362999, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 101050932, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13067478, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4756064, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 371.798039, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 188, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.745346, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.612058, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974829, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 144.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 135, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.81, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.45, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.69, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 165, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 346.360986, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.60151, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.28, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.54199240920947, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.19, "STAR_mqc-generalstats-star-uniquely_mapped": 256941061, "fastp_mqc-generalstats-fastp-pct_duplication": 43.8164, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973774, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 68821041300, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 539858052, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.560702, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49977007028092, "fastp_mqc-generalstats-fastp-pct_adapter": 56.73817379971834, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 144.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.91809014270292, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 264309347, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.27915778766284, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 274040260, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.635859359056, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 274040260, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.2826878302953, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.8380619689266, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 269929026, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.2826878302953, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.8380619689266, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 269929026 }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.7835611821461, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.97400763784478, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 269929026, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.7835611821461, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.97400763784478, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 269929026 }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 180090674, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590610852, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007518, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.651489, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 205834371, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.914724, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.952836, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.063705, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.047164, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 188281585, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 95056798, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13112709, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4705222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 359.337063, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 184, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.743266, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.608036, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974737, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0.09, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 149.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 139, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.9, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.49, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.87, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.74, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 177, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 405.323519, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.656424, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2184, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.84732621820002, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.27, "STAR_mqc-generalstats-star-uniquely_mapped": 281335868, "fastp_mqc-generalstats-fastp-pct_duplication": 49.1549, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973719, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75850054111, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590610852, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.554514, "fastp_mqc-generalstats-fastp-pct_surviving": 98.435142, "fastp_mqc-generalstats-fastp-pct_adapter": 54.403712000000006, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 149.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.81432732631198, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288851016, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.34297213023945, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 408953705, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.34477635774894, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 408953705, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.10666744455307, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.8223361463057, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295305426, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.10666744455307, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.8223361463057, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295305426 }, { "Sample": "659_dts-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.4293549270471, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.9493885527183, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295305426, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.4293549270471, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.9493885527183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295305426 }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 155123969, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589604712, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005878, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.686319, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 184947706, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.923699, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.961011, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.057561, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.038989, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 170835965, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 86251675, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10645828, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3499342, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 347.796174, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 90, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.660637, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.482097, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.971246, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 159.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.68, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.99, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 224, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 482.104395, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.690377, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.7231, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.4128392738684, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.04, "STAR_mqc-generalstats-star-uniquely_mapped": 283114655, "fastp_mqc-generalstats-fastp-pct_duplication": 51.4477, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.970104, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78200808659, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589604712, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.608866, "fastp_mqc-generalstats-fastp-pct_surviving": 98.267452, "fastp_mqc-generalstats-fastp-pct_adapter": 44.51050933333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 159.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.31063833153355, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289822078, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.8897888144782, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 483077510, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.54273239392994, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 483077510, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.21276641057013, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.6588258168466, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294802356, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.21276641057013, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.6588258168466, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294802356 }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.3799390469274, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 61, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.7679056235222, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294802356, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.3799390469274, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 61, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.7679056235222, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294802356 }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 117049101, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589492568, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005873, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.767735, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 136918684, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.906686, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.950509, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.068027, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.049491, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 124142215, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 62604226, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 9314104, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3259700, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 244.721912, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 61, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.613052, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.41003, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.972299, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 155.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.68, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.91, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.11, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 216, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 453.193561, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.772271, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6919, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.87862706433862, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.91, "STAR_mqc-generalstats-star-uniquely_mapped": 282681922, "fastp_mqc-generalstats-fastp-pct_duplication": 57.682599999999994, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971212, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76854980735, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589492568, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.612707, "fastp_mqc-generalstats-fastp-pct_surviving": 98.24876133333333, "fastp_mqc-generalstats-fastp-pct_adapter": 48.7815885, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 155.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.25362717719624, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289598915, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 91.8797070219953, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 426572365, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.41356669743844, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 426572365, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.04091996013729, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.16994283123856, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294746284, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.04091996013729, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.16994283123856, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294746284 }, { "Sample": "659_eHw-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.04510063906486, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 61, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.29653305824206, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294746284, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.04510063906486, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 61, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.29653305824206, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294746284 }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 355461595, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 540181198, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005402, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.452543, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 295726141, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.936306, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.965781, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.053828, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.034219, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 276890083, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 140292117, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15918237, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4970689, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 588.233182, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 281, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.760089, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.648525, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975531, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 162.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 149, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.33, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.52, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 218, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 564.367499, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.455, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1426, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.0912934486793, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.91, "STAR_mqc-generalstats-star-uniquely_mapped": 259032830, "fastp_mqc-generalstats-fastp-pct_duplication": 34.025499999999994, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974604, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 71735988632, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 540181198, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.544495, "fastp_mqc-generalstats-fastp-pct_surviving": 98.61642978426458, "fastp_mqc-generalstats-fastp-pct_adapter": 43.86705129751754, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 162.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.93147224646646, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 264503700, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.10855377691956, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 273879920, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.80895474818695, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 273879920, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.16116302694394, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.20274865620183, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270090599, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.16116302694394, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.20274865620183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 270090599 }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.89919298749521, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 136.30517842274102, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270090599, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.89919298749521, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 136.30517842274102, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 270090599 }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 308195964, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 455111232, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005375, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.442014, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 253945574, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.936778, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.968964, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.05359, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.031036, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 237890511, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 120824118, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13608953, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3870026, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 533.146964, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 245, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.748737, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.632498, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974443, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 179.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 162, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.59, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 280, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 791.2502090000002, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.444403, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1327, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.52913621759512, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.01, "STAR_mqc-generalstats-star-uniquely_mapped": 218471953, "fastp_mqc-generalstats-fastp-pct_duplication": 33.861999999999995, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973515, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 61985270071, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 455111232, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.543787, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49431170107957, "fastp_mqc-generalstats-fastp-pct_adapter": 35.71300754894062, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 179.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.84435599251482, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 222650327, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.0624241119803, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 231034272, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.58639972331517, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 231034272, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.11286182863127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.8614438283079, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227555616, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.11286182863127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.8614438283079, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 227555616 }, { "Sample": "659_ecd-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.79708230340069, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.9336136577706, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227555616, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.79708230340069, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.9336136577706, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 227555616 }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 202585948, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589179086, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006771, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.613557, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 227684165, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.919173, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.958557, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.063304, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.041443, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 209281144, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 106096163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14413411, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4587048, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 437.71787, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 205, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.728817, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.610807, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973483, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 166.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 153, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.34, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.17, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 211, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 448.148512, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.61774, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.33709999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 86.82481778287988, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.61, "STAR_mqc-generalstats-star-uniquely_mapped": 278708367, "fastp_mqc-generalstats-fastp-pct_duplication": 47.288999999999994, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972392, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79395630134, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589179086, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.567027, "fastp_mqc-generalstats-fastp-pct_surviving": 98.19651433333333, "fastp_mqc-generalstats-fastp-pct_adapter": 40.16421883333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 166.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.60094267840321, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 287522171, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.88471462113127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 420825744, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.76492268330907, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 420825744, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.36856331494599, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.53139758935706, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294589543, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.36856331494599, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 56, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.53139758935706, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294589543 }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.84401364519437, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.61985917809716, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294589543, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.84401364519437, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.61985917809716, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294589543 }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 143468675, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 588125580, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007068, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.738904, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 153557070, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.897128, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.947894, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.075803, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.052106, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 137760323, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 69786234, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11640021, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3836156, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 282.209423, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 123, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.684692, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.537488, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97293, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 167.4, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 154, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.37, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.36, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.59, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 211, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 437.945855, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.744164, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.4192, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 86.22924593877013, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.4, "STAR_mqc-generalstats-star-uniquely_mapped": 277597182, "fastp_mqc-generalstats-fastp-pct_duplication": 59.38440000000001, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971807, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79091172184, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 588125580, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.575616, "fastp_mqc-generalstats-fastp-pct_surviving": 98.02092999999999, "fastp_mqc-generalstats-fastp-pct_adapter": 40.427722333333335, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 167.4, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.60860325102676, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 287030582, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.91480711004559, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 336868861, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.02998018096714, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 336868861, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.1651546910604, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.32746654209464, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294062790, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 88.1651546910604, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.32746654209464, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294062790 }, { "Sample": "659_epP-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.78672973753534, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.42289592641083, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294062790, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.78672973753534, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.42289592641083, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294062790 }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 354481274, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591795694, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006213, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.481683, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 306738023, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.937113, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.965803, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.0509, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.034197, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 287448017, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 145247340, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15613036, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 5142858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 575.304575, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 277, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.749762, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.644658, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974905, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 152.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 140, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.49, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.94, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 192, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 459.031002, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.484694, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2641, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.06753333173187, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.51, "STAR_mqc-generalstats-star-uniquely_mapped": 282626281, "fastp_mqc-generalstats-fastp-pct_duplication": 33.85, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973969, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 76319299861, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591795694, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.548492, "fastp_mqc-generalstats-fastp-pct_surviving": 98.63261566666667, "fastp_mqc-generalstats-fastp-pct_adapter": 52.20279216666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 152.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.83189906075931, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289482483, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.59357619718564, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361954601, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.21165500045976, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361954601, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.15803169606119, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.34376688452215, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295897847, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.15803169606119, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.34376688452215, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295897847 }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.8643343147211, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 132.46079900338037, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 147, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295897847, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.8643343147211, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 132.46079900338037, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 147, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295897847 }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 236806824, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590959336, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006554, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.570862, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 253603353, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.929089, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.962662, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055639, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.037338, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 235620129, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 119186408, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14110114, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4622849, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 478.838697, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 222, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.732872, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.618202, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97469, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 158.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 147, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.58, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.67, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.86, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 215, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 527.74117, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.574628, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.2123, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.25782268121037, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.54, "STAR_mqc-generalstats-star-uniquely_mapped": 282310744, "fastp_mqc-generalstats-fastp-pct_duplication": 42.7382, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973704, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 77822244580, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590959336, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.550979, "fastp_mqc-generalstats-fastp-pct_surviving": 98.49322266666667, "fastp_mqc-generalstats-fastp-pct_adapter": 47.499531833333336, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 158.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.64291091595514, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288514949, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.00719276737499, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 453442873, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.16681001901784, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 453442873, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.06578191017068, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.1879893509289, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295479668, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.06578191017068, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.1879893509289, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295479668 }, { "Sample": "659_ezg-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.644034167769, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 135.2870206115163, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295479668, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.644034167769, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 135.2870206115163, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295479668 }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 309032942, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591390610, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.0059, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.508257, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 290812039, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.932059, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.966582, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055944, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.033418, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 271053883, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 137653592, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 16269091, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4759138, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 593.312195, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 258, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.723415, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.619848, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974379, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 172.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 158, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 235, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 598.230978, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.511274, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.8895, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.98699950752234, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.91, "STAR_mqc-generalstats-star-uniquely_mapped": 280638549, "fastp_mqc-generalstats-fastp-pct_duplication": 39.256299999999996, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973391, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 80170919914, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591390610, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.542781, "fastp_mqc-generalstats-fastp-pct_surviving": 98.56510166666666, "fastp_mqc-generalstats-fastp-pct_adapter": 37.87040783333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 172.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.88691808955167, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289447021, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.80660670924149, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 375301244, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.38216296869626, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 375301244, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.14388730618843, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.22440799660313, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295695305, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.14388730618843, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.22440799660313, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295695305 }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.951347997564, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 139.30152434784176, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295695305, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.951347997564, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 139.30152434784176, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295695305 }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 195875134, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590827346, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006048, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.621722, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 223496882, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.920827, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.959493, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.063186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.040507, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 205801952, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 104510560, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14121792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4412106, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 435.095995, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 181, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.696017, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.579147, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 167.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 152, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.53, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.6, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.82, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 221, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 543.684545, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.625505, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.939, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.03991939600532, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.95, "STAR_mqc-generalstats-star-uniquely_mapped": 280490714, "fastp_mqc-generalstats-fastp-pct_duplication": 48.030899999999995, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973856, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 78914007969, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590827346, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546627, "fastp_mqc-generalstats-fastp-pct_surviving": 98.47122433333332, "fastp_mqc-generalstats-fastp-pct_adapter": 41.8055545, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 167.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.89043142901514, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289181719, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.7622502874144, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 367989892, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.97652790506866, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 367989892, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.2810765874618, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.10008996773823, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295413673, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.2810765874618, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.10008996773823, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295413673 }, { "Sample": "659_gK-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.78214436995952, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.18970947901929, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295413673, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.78214436995952, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.18970947901929, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295413673 }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 385722251, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 473600946, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005356, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.423695, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 272938635, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.937897, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.967767, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.05281, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.032233, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 255988191, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 129824715, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 14413839, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4323955, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 560.554432, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 244, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.750051, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.634906, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.976063, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 171.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 156, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.28, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.48, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 246, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 688.854061, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.425976, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.89489999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.83434628071161, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.31, "STAR_mqc-generalstats-star-uniquely_mapped": 228068710, "fastp_mqc-generalstats-fastp-pct_duplication": 32.2241, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.975167, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 63711922130, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 473600946, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.534806, "fastp_mqc-generalstats-fastp-pct_surviving": 98.61008652742967, "fastp_mqc-generalstats-fastp-pct_adapter": 39.88093942710136, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 171.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.85230116495586, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 231714712, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.7409572493681, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 240138186, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.93727068507663, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 240138186, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.73402823386469, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.90239429547086, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 236800473, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.73402823386469, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.90239429547086, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 236800473 }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.05565766338296, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 137.99007781542733, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 236800473, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.05565766338296, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 137.99007781542733, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 236800473 }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 245132651, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591237046, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005468, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.558409, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 261084971, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.926976, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.961962, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.06064, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.038038, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 242019555, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 122945708, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15832305, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4861547, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 529.531455, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 227, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.743832, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.626025, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975162, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 174.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 158, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.19, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.31, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.12, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.54, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 260, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 722.381617, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.561479, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.8719, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 91.91250388600902, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.35, "STAR_mqc-generalstats-star-uniquely_mapped": 284838171, "fastp_mqc-generalstats-fastp-pct_duplication": 43.592, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974237, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 79788799800, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591237046, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.540228, "fastp_mqc-generalstats-fastp-pct_surviving": 98.53950766666667, "fastp_mqc-generalstats-fastp-pct_adapter": 38.480127333333336, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_2_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 174.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.78196138271078, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289061590, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.87115719159652, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361370207, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_2_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.97276862167578, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 361370207, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_2_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.5910396420443, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.47514516876197, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295618523, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.5910396420443, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.47514516876197, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295618523 }, { "Sample": "659_rd-T1-TRNA-1_A23MVY2LT4_2_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.89153860534215, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 138.55517753872277, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295618523, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.89153860534215, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 138.55517753872277, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295618523 }, { "Sample": "FFPE_HD789_01_RNA_13_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 493532943, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 512573856, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005491, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.388855, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 313257078, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.943123, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.975739, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.047892, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.024261, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 295440108, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 150143084, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 15002380, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3733130, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 685.333758, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 274, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.713192, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.615194, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974315, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Yes", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 62.22, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 188.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 171, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.69, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.76, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.97, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 354, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 1022.177744, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.391002, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.46249999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.62413812422263, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.08, "STAR_mqc-generalstats-star-uniquely_mapped": 246247376, "fastp_mqc-generalstats-fastp-pct_duplication": 29.5777, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973399, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 70181275242, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 512573856, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.547517, "fastp_mqc-generalstats-fastp-pct_surviving": 98.56009432962855, "fastp_mqc-generalstats-fastp-pct_adapter": 32.50729928948392, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_HD789_01_RNA_13_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 188.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.958011342662, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 251053578, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.45208949988145, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 260031131, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_HD789_01_RNA_13_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.20739831443366, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 260031131, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_HD789_01_RNA_13_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.49074092682201, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 140.62043315373464, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 256286928, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 83.49074092682201, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 140.62043315373464, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 256286928 }, { "Sample": "FFPE_HD789_01_RNA_13_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.31868870026548, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 140.69150659919728, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 256286928, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.31868870026548, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 140.69150659919728, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 256286928 }, { "Sample": "FFPE_V4_0002_RNA_0006_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 318186658, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590517774, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006866, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.515555, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 286073265, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.927308, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.966144, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.058519, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.033856, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 265278038, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 135029091, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 16740784, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4731767, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 589.608653, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 150, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.605329, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.5298, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973517, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 178.5, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 164, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.98, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.18, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.36, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 271, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 742.681637, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.519119, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.3378, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.91640564034243, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.77, "STAR_mqc-generalstats-star-uniquely_mapped": 282769773, "fastp_mqc-generalstats-fastp-pct_duplication": 39.7997, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972349, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 80726525363, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590517774, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.543074, "fastp_mqc-generalstats-fastp-pct_surviving": 98.419629, "fastp_mqc-generalstats-fastp-pct_adapter": 34.2868195, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_V4_0002_RNA_0006_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 178.5, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.82331627836828, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 285879446, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.7177967013117, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 346754944, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_V4_0002_RNA_0006_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.31590526159142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 346754944, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "FFPE_V4_0002_RNA_0006_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.7043935507862, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 140.5397805350394, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295258887, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.7043935507862, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 140.5397805350394, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295258887 }, { "Sample": "FFPE_V4_0002_RNA_0006_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.57299774605968, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 140.63312664319568, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295258887, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.57299774605968, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 140.63312664319568, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295258887 }, { "Sample": "NTC_0001_0001_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 1993, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 1682, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.626635, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.148633, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 1432, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.043994, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.185792, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.219972, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.814208, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 63, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 34, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 315, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 149, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 9.2e-05, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 0, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.93204, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "Skipped", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": "N/A", "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 81.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 72, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 3.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 3.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 9.89, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 9.89, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 32, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 35.04918, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.398089, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0.3594, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 33.7866, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 2.8825205295793532, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 9.39, "STAR_mqc-generalstats-star-uniquely_mapped": 79, "fastp_mqc-generalstats-fastp-pct_duplication": 44.029, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.885273, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 161943, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 1682, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.712677, "fastp_mqc-generalstats-fastp-pct_surviving": 2.4798018517426432, "fastp_mqc-generalstats-fastp-pct_adapter": 50.10025358259126, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "NTC_0001_0001_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 81.1818, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 9.512485136741974, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 80, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 96.96585480922333, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 76, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 54.54545454545454, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 33914, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "NTC_0001_0001_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 95.38243793123783, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 98, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 54.54545454545454, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 33914, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "NTC_0001_0001_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 34.958382877526745, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 67, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 108.06183115338882, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 45.45454545454545, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 841, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 34.958382877526745, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 67, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 108.06183115338882, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 45.45454545454545, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 841 }, { "Sample": "NTC_0001_0001_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 42.92508917954816, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 75, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 109.53388822829965, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 45.45454545454545, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 841, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 42.92508917954816, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 75, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 109.53388822829965, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 45.45454545454545, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 841 }, { "Sample": "PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 265943868, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 591605900, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005262, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.54912, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 266743033, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.936663, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.963512, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.051665, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.036488, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 249848414, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 126023861, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13781338, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4772553, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 474.03279, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 196, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.706131, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.595395, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97605, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 143.6, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 135, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.32, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 4.18, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.9, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 160, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 352.451812, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.552025, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.5274, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.64138477419004, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 96.01, "STAR_mqc-generalstats-star-uniquely_mapped": 283990316, "fastp_mqc-generalstats-fastp-pct_duplication": 38.0923, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97509, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75057397787, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 591605900, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.54264, "fastp_mqc-generalstats-fastp-pct_surviving": 98.60098333333333, "fastp_mqc-generalstats-fastp-pct_adapter": 57.50015616666667, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 143.6, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.2713204854786, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290689465, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.50335735663717, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 391255470, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.4204447055192, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 391255470, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.61744773061352, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.03558653826812, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295802950, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.61744773061352, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.03558653826812, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295802950 }, { "Sample": "PX_FFPE_bld_TRNA_nat_01_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.70707985248536, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.17368911635262, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295802950, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.70707985248536, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.17368911635262, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295802950 }, { "Sample": "PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 140801160, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 581201710, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006391, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.720981, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 162166354, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.911127, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.945834, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.065967, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.054166, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 147754102, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 74203312, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10697616, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4249465, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 247.8056, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 92, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.640676, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.486372, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975049, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 130.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 124, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.98, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.09, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.15, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 134, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 221.102211, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.725619, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.41680000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.82024299490423, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.68, "STAR_mqc-generalstats-star-uniquely_mapped": 278038265, "fastp_mqc-generalstats-fastp-pct_duplication": 49.0301, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973842, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 70271828618, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 581201710, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.54692, "fastp_mqc-generalstats-fastp-pct_surviving": 98.31343028450243, "fastp_mqc-generalstats-fastp-pct_adapter": 69.11044395754968, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 130.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.19177063329701, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 285346125, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.58032061883574, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295586121, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.30759885291403, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295586121, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.60646623622407, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.04845203225572, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 290600855, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.60646623622407, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.04845203225572, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 290600855 }, { "Sample": "PX_FFPE_bld_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.60352977510843, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.248597382826, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 290600855, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.60352977510843, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.248597382826, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 290600855 }, { "Sample": "PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 202052096, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590808070, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.005898, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.607231, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 232051368, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.927583, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.958142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.057401, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.041858, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 215246791, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 108583996, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 13320086, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4743697, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 410.297326, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 167, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.700321, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.578875, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975177, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 145.3, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 136, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.1, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.63, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.54, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.95, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 160, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 334.284351, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.610833, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1621, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.29473193357425, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.92, "STAR_mqc-generalstats-star-uniquely_mapped": 283345716, "fastp_mqc-generalstats-fastp-pct_duplication": 43.626, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97413, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75610298051, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590808070, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.543601, "fastp_mqc-generalstats-fastp-pct_surviving": 98.46801166666667, "fastp_mqc-generalstats-fastp-pct_adapter": 55.645601666666664, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 145.3, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.0508604088634, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289646198, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.21254822176849, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 396121399, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.00723328319253, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 396121399, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.25080885382529, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.30118159354188, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295404035, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.25080885382529, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.30118159354188, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295404035 }, { "Sample": "PX_FFPE_bld_TRNA_nat_03_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.35959719999647, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.437432924706, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295404035, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.35959719999647, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.437432924706, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295404035 }, { "Sample": "PX_FFPE_bld_TRNA_nat_04_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 139806567, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590126794, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006017, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.734245, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 156829212, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.911612, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.947884, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.065746, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.052116, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 142967370, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 71859203, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10310854, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3950938, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 251.024266, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 106, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.670442, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.512441, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973005, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 136.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 129, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.11, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 1.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 146, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 286.307918, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.73869, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.6058, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 90.20500136813635, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.89, "STAR_mqc-generalstats-star-uniquely_mapped": 282939217, "fastp_mqc-generalstats-fastp-pct_duplication": 51.5614, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97192, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 73085110383, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590126794, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546824, "fastp_mqc-generalstats-fastp-pct_surviving": 98.35446566666667, "fastp_mqc-generalstats-fastp-pct_adapter": 63.518898333333325, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_04_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 136.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.31176721658905, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 290082040, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.26350893331106, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 376033679, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_04_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.85863109310954, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 376033679, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_bld_TRNA_nat_04_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.77006726290622, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.33083364454046, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295063397, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.77006726290622, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.33083364454046, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295063397 }, { "Sample": "PX_FFPE_bld_TRNA_nat_04_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.70850136045297, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 127.50469190863413, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295063397, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.70850136045297, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 127.50469190863413, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295063397 }, { "Sample": "PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 116638841, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589216832, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006619, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.768656, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 136312057, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.902599, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.943971, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.068788, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.056029, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 123035147, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 61816270, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 9376623, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3669052, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 208.853897, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 92, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.665979, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.48268, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974956, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 132, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 125, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.93, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.48, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 138, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 242.71279600000003, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.773778, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.4118, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.43846777616886, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.44, "STAR_mqc-generalstats-star-uniquely_mapped": 281185575, "fastp_mqc-generalstats-fastp-pct_duplication": 56.721999999999994, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973767, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 71714572915, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589216832, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.544437, "fastp_mqc-generalstats-fastp-pct_surviving": 98.20280533333333, "fastp_mqc-generalstats-fastp-pct_adapter": 66.80828149999999, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 132, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.19324950988502, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289285577, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.66527340072453, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 343252576, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.27648580836299, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 343252576, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.74650194135957, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 124.89096062347384, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294608416, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.74650194135957, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 124.89096062347384, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294608416 }, { "Sample": "PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.63159784991659, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.07656970329049, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294608416, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.63159784991659, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.07656970329049, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294608416 }, { "Sample": "PX_FFPE_gb_TRNA_nat_01_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 188477457, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 523873694, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006973, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.597754, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 210725942, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.926019, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.957169, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.056646, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.042831, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 195136194, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 98249155, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11936768, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4396448, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 360.451635, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 181, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.736093, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.607396, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975506, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 140.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 133, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.35, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.11, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 149, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 263.682723, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.601952, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.1067, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.03916862644013, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.5, "STAR_mqc-generalstats-star-uniquely_mapped": 247537885, "fastp_mqc-generalstats-fastp-pct_duplication": 43.4356, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974436, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 66216888245, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 523873694, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553514, "fastp_mqc-generalstats-fastp-pct_surviving": 98.41086407401777, "fastp_mqc-generalstats-fastp-pct_adapter": 59.37235565051897, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_01_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 140.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.20320353783598, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 257230375, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.59693122728856, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 266166596, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_01_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.15261235990359, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 266166596, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_01_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.60497652757488, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.63235681767216, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 261936847, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.60497652757488, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.63235681767216, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 261936847 }, { "Sample": "PX_FFPE_gb_TRNA_nat_01_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.4305143750975, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 129.78266609050235, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 137, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 261936847, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 84.4305143750975, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 129.78266609050235, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 137, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 261936847 }, { "Sample": "PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 138839805, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589255236, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.009915, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.699458, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 177095898, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.901407, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.949376, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.065602, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.050624, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 159635483, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 80430296, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11617854, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4288797, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 297.511859, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 143, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.72349, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.572646, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974165, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 145.1, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 136, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.33, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.56, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 153, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 254.94111, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.706463, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.7055, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.74915285888424, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.44, "STAR_mqc-generalstats-star-uniquely_mapped": 275302478, "fastp_mqc-generalstats-fastp-pct_duplication": 51.02759999999999, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.972861, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 74962989791, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589255236, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.574718, "fastp_mqc-generalstats-fastp-pct_surviving": 98.20920600000001, "fastp_mqc-generalstats-fastp-pct_adapter": 56.35153233333333, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 145.1, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.9422485776605, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288564914, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.37515374308391, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 56, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 363984098, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.99077904931525, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 363984098, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.03595999572372, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.67591764258842, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294627618, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.03595999572372, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.67591764258842, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294627618 }, { "Sample": "PX_FFPE_gb_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.10233483188757, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.8410033271219, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294627618, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.10233483188757, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 57, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.8410033271219, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 18.181818181818183, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294627618 }, { "Sample": "PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 41069821, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 220127548, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007242, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.818093, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 40042751, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.851597, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.899249, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.108593, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.100752, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 34100284, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 17068194, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 4348347, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 1912315, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 48.947777, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 21, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.427027, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.126971, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974443, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 117.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 114, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.07, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.67, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.31, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.14, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.91, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.44, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 118, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 171.917223, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.824061, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.99940000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.2110556897268, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.96, "STAR_mqc-generalstats-star-uniquely_mapped": 104512567, "fastp_mqc-generalstats-fastp-pct_duplication": 51.0562, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97317, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 24771882950, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 220127548, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.54921, "fastp_mqc-generalstats-fastp-pct_surviving": 98.04663957734886, "fastp_mqc-generalstats-fastp-pct_adapter": 80.49075292702967, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 117.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.67349427796287, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 107503134, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.11455412682542, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 112256549, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.88146614801228, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 112256549, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.10270825916916, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 115.49352699826557, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 117, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 110063774, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.10270825916916, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 115.49352699826557, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 117, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 110063774 }, { "Sample": "PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.04121784006966, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 115.76835655299263, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 117, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 110063774, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.04121784006966, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 115.76835655299263, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 117, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 110063774 }, { "Sample": "PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 74604231, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 557404190, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.0086, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.859623, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 78246677, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.816133, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.885633, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.122602, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.114367, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 63859710, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 32029863, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 9593228, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4136212, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 99.021782, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 25, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.472084, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.243889, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973016, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 126, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 121, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.46, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.55, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.29, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.79, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 128, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 184.526006, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.86708, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.9161, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.91390245911593, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.51, "STAR_mqc-generalstats-star-uniquely_mapped": 263395866, "fastp_mqc-generalstats-fastp-pct_duplication": 58.4393, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971123, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 65633834794, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 557404190, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.606657, "fastp_mqc-generalstats-fastp-pct_surviving": 97.91650457162645, "fastp_mqc-generalstats-fastp-pct_adapter": 72.32099137217682, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 126, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.38224357445178, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 271406353, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.49547940383917, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 284632398, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.85244207570284, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 59, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 284632398, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.57113408198873, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 121.09303630817702, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 278702095, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.57113408198873, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 121.09303630817702, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 278702095 }, { "Sample": "PX_FFPE_kid_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.42919241442792, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 60, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 121.39540880379819, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 278702095, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.42919241442792, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 60, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 121.39540880379819, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 278702095 }, { "Sample": "PX_FFPE_kid_TRNA_nat_03_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 6221904, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 30609244, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.009221, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.817189, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 5595717, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.823708, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.879488, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.125851, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.120512, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 4609235, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 2303496, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 704224, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 315636, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 5.99177, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 1, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.035343, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.005094, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973071, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 108.9, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 105, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.44, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.08, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 1.9, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.62, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 106, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 134.715835, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.824794, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 9.999999999999999e-05, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.7966, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 82.9445533650978, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.45, "STAR_mqc-generalstats-star-uniquely_mapped": 14302248, "fastp_mqc-generalstats-fastp-pct_duplication": 45.2151, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97134, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 3208100783, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 30609244, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.58321, "fastp_mqc-generalstats-fastp-pct_surviving": 95.02354878910747, "fastp_mqc-generalstats-fastp-pct_adapter": 85.96307953689202, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_03_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 108.9, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 96.95084269314198, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 14837960, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.1142720849894, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 57, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 36.36363636363637, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 16106136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_03_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.38422451594701, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 36.36363636363637, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 16106136, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_kid_TRNA_nat_03_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.5849367089962, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 107.69751288205616, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 107, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 15304622, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.5849367089962, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 58, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 107.69751288205616, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 107, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 15304622 }, { "Sample": "PX_FFPE_kid_TRNA_nat_03_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 82.33202980770905, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 58, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 108.09517405918291, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 107, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 15304622, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 82.33202980770905, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 58, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 108.09517405918291, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 107, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 15304622 }, { "Sample": "PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 58644573, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 461742130, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.007583, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.859608, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 64824812, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.843101, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.907715, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.102883, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.092285, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 54653854, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 27445528, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 6669365, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2790304, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 92.221156, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 29, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.499913, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.23136, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974944, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 134.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 127, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.28, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.57, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.38, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 153, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 377.611721, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.866177, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.307, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 81.51991761088753, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 92.05, "STAR_mqc-generalstats-star-uniquely_mapped": 212518796, "fastp_mqc-generalstats-fastp-pct_duplication": 60.287400000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973148, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 56452513634, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 461742130, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.539334, "fastp_mqc-generalstats-fastp-pct_surviving": 98.21712470780997, "fastp_mqc-generalstats-fastp-pct_adapter": 66.44294597501086, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 134.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.12184201168735, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 224226231, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.59242064491438, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 235061926, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.05064949352271, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 235061926, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.64893921038868, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.5116528136603, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 230871065, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.64893921038868, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.5116528136603, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 230871065 }, { "Sample": "PX_FFPE_pan_TRNA_nat_01_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.44142636198306, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.74087771458065, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 230871065, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.44142636198306, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.74087771458065, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 230871065 }, { "Sample": "PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 60087708, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 446469968, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.009641, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.861587, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 61797160, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.810186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.885645, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.12016, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.114355, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 50067171, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 25086417, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 7425565, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 3239179, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 78.367985, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 29, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.495315, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.204631, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.973163, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 126.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 120, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.15, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.23, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.04, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.71, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.31, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 130, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 226.771799, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.869975, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.64059999999999, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 80.57075930122825, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 91.98, "STAR_mqc-generalstats-star-uniquely_mapped": 205326872, "fastp_mqc-generalstats-fastp-pct_duplication": 56.437000000000005, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.971172, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 52582860047, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 446469968, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.546248, "fastp_mqc-generalstats-fastp-pct_surviving": 98.20842454261502, "fastp_mqc-generalstats-fastp-pct_adapter": 73.65883856285221, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 126.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.02564719873835, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 216595188, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.8836412861475, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227307367, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 88.15350321517775, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 227307367, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 90.01718499656742, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 121.12787815999306, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 223234984, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 90.01718499656742, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 121.12787815999306, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 223234984 }, { "Sample": "PX_FFPE_pan_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 89.5789416488519, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 121.40039303606643, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 223234984, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 89.5789416488519, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 121.40039303606643, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 223234984 }, { "Sample": "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 145763366, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 562945688, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006764, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.677617, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 181484166, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.919408, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.953365, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.05961, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.046635, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 166858062, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 83899157, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 10818305, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4104017, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 292.567364, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 120, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.684546, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.532142, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975611, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 134.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 127, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 2.13, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.47, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 5.21, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.65, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 152, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 353.772265, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.682232, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.566, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.71900338098642, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.82, "STAR_mqc-generalstats-star-uniquely_mapped": 266897825, "fastp_mqc-generalstats-fastp-pct_duplication": 46.1137, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.974337, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 68845680093, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 562945688, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.536669, "fastp_mqc-generalstats-fastp-pct_surviving": 98.3470923300022, "fastp_mqc-generalstats-fastp-pct_adapter": 66.38576696910273, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 134.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.82222898916672, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 275343010, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.10247512575936, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 286203524, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 83.80650167668136, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 286203524, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.15610756378427, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.41374446410184, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 281472844, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.15610756378427, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.41374446410184, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 281472844 }, { "Sample": "PX_FFPE_pan_TRNA_nat_03_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.18190721423122, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 125.60544579213474, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 132, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 281472844, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.18190721423122, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 125.60544579213474, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 132, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 281472844 }, { "Sample": "PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 124133890, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 531990824, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006562, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.747359, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 134402616, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.888291, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.924938, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.085737, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.075062, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 119388667, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 59935219, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11523256, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4863982, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 192.653635, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 99, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.687725, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.499556, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.976303, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 128, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 121, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.01, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 1.19, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.45, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 3.61, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.7, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 130, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 210.872937, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.752295, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.5765, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 88.81071181327954, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 95.38, "STAR_mqc-generalstats-star-uniquely_mapped": 253706104, "fastp_mqc-generalstats-fastp-pct_duplication": 53.7845, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.975099, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 63358500423, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 531990824, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.539305, "fastp_mqc-generalstats-fastp-pct_surviving": 98.24477910205611, "fastp_mqc-generalstats-fastp-pct_adapter": 70.97846074967134, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 128, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.71081126767706, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 259906275, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.72256993838755, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270747631, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 84.65716058548915, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 270747631, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.78153604564997, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 122.02891899503891, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 265995412, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.78153604564997, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 122.02891899503891, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 265995412 }, { "Sample": "PX_FFPE_pst_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.92053239888698, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 122.23508809994061, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 127, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 265995412, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.92053239888698, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 54, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 122.23508809994061, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 127, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 265995412 }, { "Sample": "PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 138640455, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 590422322, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008532, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.711485, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 170345832, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.901323, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.946029, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.069106, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.053971, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 153536633, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 77402649, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11772003, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4415831, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 287.088544, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 132, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.704615, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.550308, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.975045, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 145.2, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 137, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.73, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.27, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.07, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.14, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.4, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 166, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 362.695162, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.717607, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.9145, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 85.06152310131925, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.57, "STAR_mqc-generalstats-star-uniquely_mapped": 276238598, "fastp_mqc-generalstats-fastp-pct_duplication": 52.5374, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.97375, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 75713875755, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 590422322, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.554937, "fastp_mqc-generalstats-fastp-pct_surviving": 98.40372033333334, "fastp_mqc-generalstats-fastp-pct_adapter": 55.80212783333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 145.2, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.86281284940985, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 288901946, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.02818319582416, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 303261243, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.73226668884163, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 303261243, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 87.01670459249648, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.60646324615078, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295211161, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 87.01670459249648, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.60646324615078, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295211161 }, { "Sample": "PX_FFPE_stm_TRNA_nat_01_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.94131464569193, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 131.7659848910658, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 295211161, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 86.94131464569193, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 131.7659848910658, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 295211161 }, { "Sample": "PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 134894619, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 331671720, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.008476, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.567079, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 143587602, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.924385, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.96073, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.056036, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.03927, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 132730244, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 67017579, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 8046006, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 2739352, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 263.821236, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 119, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.69135, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.533042, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.974751, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 154.8, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 144, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.77, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.28, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.06, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.31, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.42, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 181, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 409.68298, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.571927, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 96.70570000000001, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 84.82035914715821, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 93.48, "STAR_mqc-generalstats-star-uniquely_mapped": 155018059, "fastp_mqc-generalstats-fastp-pct_duplication": 41.55, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973374, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 43409900436, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 331671720, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553422, "fastp_mqc-generalstats-fastp-pct_surviving": 98.37063342624323, "fastp_mqc-generalstats-fastp-pct_adapter": 49.727784032868385, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 154.8, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 97.75638031484867, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 162115134, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.69950104707644, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168582690, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 80.72562608667454, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 168582690, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.73013832755979, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.3755720385205, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 165835860, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 81.73013832755979, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.3755720385205, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 165835860 }, { "Sample": "PX_FFPE_stm_TRNA_nat_02_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 81.93946851923364, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 55, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 134.53485445186584, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 165835860, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 81.93946851923364, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 55, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 134.53485445186584, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 151, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 165835860 }, { "Sample": "PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": 9999000000, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 173462335, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": 589871676, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": 0.006655, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": 0.650963, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": 205886920, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": 0.925626, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": 0.959607, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": 0.055307, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": 0.040394, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": 190574174, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": 95980479, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": 11387014, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": 4040186, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": 353.304349, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": 146, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": 0.689519, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": 0.557976, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": 0.97472, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": 0, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": "No", "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": 141.7, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 134, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.03, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": 0.99, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": 0.48, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": 0, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.05, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": 2.8, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": 0.66, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": 0, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 162, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 380.634515, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.655325, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 0, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": 97.3927, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 87.88120089628, "STAR_mqc-generalstats-star-uniquely_mapped_percent": 94.75, "STAR_mqc-generalstats-star-uniquely_mapped": 279450707, "fastp_mqc-generalstats-fastp-pct_duplication": 45.6616, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.973501, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 74758293856, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 589871676, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.535818, "fastp_mqc-generalstats-fastp-pct_surviving": 98.31194599999999, "fastp_mqc-generalstats-fastp-pct_adapter": 58.40268533333334, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": 141.7, "Kallisto_mqc-generalstats-kallisto-percent_aligned": 98.10652342629179, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 289351297, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 86.33156203360336, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 52, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 334141844, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.1838656951613, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 54, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 151, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 18.181818181818183, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 334141844, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null }, { "Sample": "PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1_trimmed_1", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.43368518484505, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.0989540477614, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294935838, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.43368518484505, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.0989540477614, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294935838 }, { "Sample": "PX_FFPE_stm_TRNA_nat_03_A23MVY2LT4_1_trimmed_2", "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null, "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_unmapped": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_dupes": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-unique_reads": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_on_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-reads_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-pairs_off_target": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-mean_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-q50_depth": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt30x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-frac_bases_gt100x": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-n_q30": null, "Custom content: SeqTools (general stats)_mqc-generalstats-custom_content_seqtools_general_stats-gc_bias": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null, "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null, "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_tpm": null, "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null, "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null, "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null, "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null, "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped_percent": null, "STAR_mqc-generalstats-star-uniquely_mapped": null, "fastp_mqc-generalstats-fastp-pct_duplication": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null, "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null, "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null, "fastp_mqc-generalstats-fastp-after_filtering_gc_content": null, "fastp_mqc-generalstats-fastp-pct_surviving": null, "fastp_mqc-generalstats-fastp-pct_adapter": null, "Kallisto_mqc-generalstats-kallisto-fragment_length": null, "Kallisto_mqc-generalstats-kallisto-percent_aligned": null, "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": null, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 85.61240161151859, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_gc": 53, "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 130.2594157479092, "FastQC (raw)_mqc-generalstats-fastqc_raw-median_sequence_length": 142, "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 9.090909090909092, "FastQC (raw)_mqc-generalstats-fastqc_raw-total_sequences": 294935838, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": 85.61240161151859, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_gc": 53, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": 130.2594157479092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": 142, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": 9.090909090909092, "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": 294935838 } ] }