{
  "source_file": "multiqc_general_stats.txt",
  "total_samples": 240,
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    "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",
    "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: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated",
    "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",
    "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",
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    "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",
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    "Kallisto_mqc-generalstats-kallisto-percent_aligned",
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    "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_fails",
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      "Custom content: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_median": 165,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_est_counts": 0.68,
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      "Custom content: RNA contamination_mqc-generalstats-custom_content_rna_contamination-contamination_pct": 66.2,
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      "Custom content: Preseq_mqc-generalstats-custom_content_preseq-expected_distinct": 409929548,
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      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": 388.91289,
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      "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": 27201065830,
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      "fastp_mqc-generalstats-fastp-after_filtering_gc_content": 0.538768,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_unmapped": null,
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      "Custom content: SeqTools_mqc-generalstats-custom_content_seqtools-frac_bases_gt100x": 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,
      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_ribo_est_counts": null,
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      "Custom content: Expression QC_mqc-generalstats-custom_content_expression_qc-pct_mito_tpm": null,
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      "Custom content: RNA contamination_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,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null,
      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_mean": null,
      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null,
      "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_RIBOSOMAL_BASES": null,
      "Picard: RnaSeqMetrics_mqc-generalstats-picard_rnaseqmetrics-PCT_MRNA_BASES": null,
      "RSeQC_mqc-generalstats-rseqc-proper_pairs_percent": null,
      "STAR_mqc-generalstats-star-uniquely_mapped_percent": null,
      "STAR_mqc-generalstats-star-uniquely_mapped": null,
      "fastp_mqc-generalstats-fastp-pct_duplication": null,
      "fastp_mqc-generalstats-fastp-after_filtering_q30_rate": null,
      "fastp_mqc-generalstats-fastp-after_filtering_q30_bases": null,
      "fastp_mqc-generalstats-fastp-filtering_result_passed_filter_reads": null,
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      "fastp_mqc-generalstats-fastp-pct_surviving": null,
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      "Kallisto_mqc-generalstats-kallisto-fragment_length": 180,
      "Kallisto_mqc-generalstats-kallisto-percent_aligned": 81.51413436397098,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_duplicates": 62.560714520354836,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-avg_sequence_length": 151,
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      "FastQC (raw)_mqc-generalstats-fastqc_raw-percent_fails": 27.27272727272727,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-percent_duplicates": null,
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      "FastQC (trimmed)_mqc-generalstats-fastqc_trimmed-total_sequences": null
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      "Sample": "FFPE_HD789_02_RNA_0005_23KKJ7LT4_1_2",
      "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: Kallisto_mqc-generalstats-custom_content_kallisto-fragment_length_mean": null,
      "Custom content: Kallisto_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: RNA contamination_mqc-generalstats-custom_content_rna_contamination-is_contaminated": null,
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      "Picard: InsertSizeMetrics_mqc-generalstats-picard_insertsizemetrics-summed_median": null,
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      "Picard: Mark Duplicates_mqc-generalstats-picard_mark_duplicates-PERCENT_DUPLICATION": null,
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