{
  "source_file": "multiqc_general_stats.txt",
  "total_samples": 240,
  "metrics": [
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    "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct",
    "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads",
    "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct",
    "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",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-unique_reads",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_dupes",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_reads_on_target",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_reads_off_target",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-n_q30",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-mean_depth",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-q50_depth",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_bases_gt30x",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_bases_gt100x",
    "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-gc_bias",
    "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"
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 65.02,
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      "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": 0.07,
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      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": 0.15,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads": 197275536,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped": 0.007377,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-unique_reads": 149238847,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_dupes": 0.2435,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_reads_on_target": 0.919996,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-n_q30": 0.971686,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-mean_depth": 284.46217,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-gc_bias": 0,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 186,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 437.962,
      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": 0.24531,
      "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": 9.999999999999999e-05,
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      "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": 89.02251646000703,
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      "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.970892,
      "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 25403340217,
      "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": 197275536,
      "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.553772,
      "fastp_mqc-generalstats-fastp-pct_surviving": 98.63776800000001,
      "fastp_mqc-generalstats-fastp-pct_adapter": 49.4966,
      "Kallisto_mqc-generalstats-kallisto-fragment_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,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null,
      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-median_sequence_length": null,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null
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    {
      "Sample": "FFPE_HD789_02_RNA_0011_23KMKGLT4_1_1",
      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null,
      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null,
      "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null,
      "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null,
      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null,
      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null,
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      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_est_counts": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null,
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      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_male_tpm": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-unique_reads": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_dupes": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_reads_on_target": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_reads_off_target": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-n_q30": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-mean_depth": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-q50_depth": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_bases_gt30x": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_bases_gt100x": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-gc_bias": null,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null,
      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null,
      "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null,
      "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null,
      "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null,
      "STAR_mqc-generalstats-star-uniquely_mapped_percent": null,
      "STAR_mqc-generalstats-star-uniquely_mapped": null,
      "fastp_mqc-generalstats-fastp-pct_duplication": null,
      "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null,
      "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null,
      "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null,
      "fastp_mqc-generalstats-fastp-after_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": 96.19024023333537,
      "Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads": 94879906,
      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 72.77488743003428,
      "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": 100000000,
      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-avg_sequence_length": null,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails": null,
      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null
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    {
      "Sample": "FFPE_HD789_02_RNA_0011_23KMKGLT4_1_2",
      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null,
      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null,
      "Custom content: Preseq_mqc-generalstats-custom_content_preseq-total_reads": null,
      "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": null,
      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null,
      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_hk_est_counts": null,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads": null,
      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped": null,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_dupes": null,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-n_q30": null,
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      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null,
      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null,
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      "STAR_mqc-generalstats-star-uniquely_mapped_percent": null,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 71.08601497419497,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null,
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null,
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      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null,
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 0,
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      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 143,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.06,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads": 197158762,
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      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": 185,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 440.0684499999999,
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      "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": 0.969605,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": null,
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": null,
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      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null,
      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": null,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": null,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped": null,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 72.16479071269126,
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 100,
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      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 31,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.02,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-reads": 995102,
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