{
    "report_data_sources": {
        "MACS2": {
            "all_sections": {
                "G207M08_narrow_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M08/fastq/bowtie2/G207M08_MACS2_output/G207M08_narrow_MACS2_peaks.xls",
                "G207M08_broad_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M08/fastq/bowtie2/G207M08_MACS2_output/G207M08_broad_MACS2_peaks.xls",
                "G207M05_narrow_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M05/fastq/bowtie2/G207M05_MACS2_output/G207M05_narrow_MACS2_peaks.xls",
                "G207M05_broad_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M05/fastq/bowtie2/G207M05_MACS2_output/G207M05_broad_MACS2_peaks.xls",
                "G207M07_broad_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M07/fastq/bowtie2/G207M07_MACS2_output/G207M07_broad_MACS2_peaks.xls",
                "G207M07_narrow_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M07/fastq/bowtie2/G207M07_MACS2_output/G207M07_narrow_MACS2_peaks.xls",
                "G207M06_narrow_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M06/fastq/bowtie2/G207M06_MACS2_output/G207M06_narrow_MACS2_peaks.xls",
                "G207M06_broad_MACS2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M06/fastq/bowtie2/G207M06_MACS2_output/G207M06_broad_MACS2_peaks.xls"
            }
        },
        "Picard": {
            "InsertSizeMetrics": {
                "G207M08_sorted_mapped": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M08/fastq/bowtie2/CollectInsertSizeMetrics/G207M08_metrics",
                "G207M05_sorted_mapped": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M05/fastq/bowtie2/CollectInsertSizeMetrics/G207M05_metrics",
                "G207M07_sorted_mapped": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M07/fastq/bowtie2/CollectInsertSizeMetrics/G207M07_metrics",
                "G207M06_sorted_mapped": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M06/fastq/bowtie2/CollectInsertSizeMetrics/G207M06_metrics"
            }
        },
        "Samtools": {
            "flagstat": {
                "flagstat_G207M08": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M08/fastq/bowtie2/flagstat_G207M08.txt",
                "flagstat_G207M05": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M05/fastq/bowtie2/flagstat_G207M05.txt",
                "flagstat_G207M07": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M07/fastq/bowtie2/flagstat_G207M07.txt",
                "flagstat_G207M06": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/G207M06/fastq/bowtie2/flagstat_G207M06.txt"
            },
            "idxstats": {
                "G207M08_idxstats": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/05_BAM_Count/Job_Summary/Chr_Read_Counts/G207M08_idxstats.out",
                "G207M05_idxstats": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/05_BAM_Count/Job_Summary/Chr_Read_Counts/G207M05_idxstats.out",
                "G207M07_idxstats": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/05_BAM_Count/Job_Summary/Chr_Read_Counts/G207M07_idxstats.out",
                "G207M06_idxstats": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/05_BAM_Count/Job_Summary/Chr_Read_Counts/G207M06_idxstats.out"
            }
        },
        "Bowtie 2 / HiSAT2": {
            "all_sections": {
                "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/04_Bowtie2/Step_04_G207_K9me3_G207M05.o43666",
                "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/04_Bowtie2/Step_04_G207_K9me3_G207M08.o43669",
                "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/04_Bowtie2/Step_04_G207_K9me3_G207M07.o43668",
                "README_Bowtie2.sh": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/04_Bowtie2/README_Bowtie2.sh",
                "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/04_Bowtie2/Step_04_G207_K9me3_G207M06.o43667"
            }
        },
        "FastQC": {
            "all_sections": {
                "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M05_FASTQC/G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R2_fastqc.zip",
                "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M05_FASTQC/G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R1_fastqc.zip",
                "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M06_FASTQC/G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R1_fastqc.zip",
                "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M06_FASTQC/G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R2_fastqc.zip",
                "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M07_FASTQC/G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R2_fastqc.zip",
                "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M07_FASTQC/G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R1_fastqc.zip",
                "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R2": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M08_FASTQC/G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R2_fastqc.zip",
                "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R1": "/projectnb2/wax-dk/max/G207_SG_CHIPSEQ_K9me3/Scripts/02_FASTQC/Job_Summary/G207M08_FASTQC/G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R1_fastqc.zip"
            }
        }
    },
    "report_general_stats_data": [
        {
            "G207M08_narrow_MACS2": {
                "peak_count": 1601,
                "fragment_size": 309.0,
                "treatment_fragments_total": 4341555.0,
                "d": 309.0
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            "G207M08_broad_MACS2": {
                "peak_count": 8276,
                "fragment_size": 309.0,
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                "d": 309.0
            },
            "G207M05_narrow_MACS2": {
                "peak_count": 1674,
                "fragment_size": 302.0,
                "treatment_fragments_total": 3072538.0,
                "d": 302.0
            },
            "G207M05_broad_MACS2": {
                "peak_count": 3256,
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                "d": 302.0
            },
            "G207M07_broad_MACS2": {
                "peak_count": 3394,
                "fragment_size": 322.0,
                "treatment_fragments_total": 3783058.0,
                "d": 322.0
            },
            "G207M07_narrow_MACS2": {
                "peak_count": 496,
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            "G207M06_narrow_MACS2": {
                "peak_count": 525,
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            },
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                "peak_count": 3009,
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                "d": 310.0
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        },
        {
            "G207M08_sorted_mapped": {
                "total_count": 4338074,
                "meansum": 1344923716.3182342,
                "total_pairs": 4338074.0,
                "summed_mean": 310.027841,
                "summed_median": 305
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            "G207M05_sorted_mapped": {
                "total_count": 3070479,
                "meansum": 928815586.547484,
                "total_pairs": 3070479.0,
                "summed_mean": 302.498596,
                "summed_median": 293
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            "G207M07_sorted_mapped": {
                "total_count": 3781092,
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                "total_pairs": 3781092.0,
                "summed_mean": 322.588925,
                "summed_median": 319
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            "G207M06_sorted_mapped": {
                "total_count": 3278759,
                "meansum": 1020380424.40906,
                "total_pairs": 3278759.0,
                "summed_mean": 311.20934,
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        },
        {
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                "mapped_failed_pct": NaN,
                "paired in sequencing_passed": 24482388,
                "paired in sequencing_failed": 0,
                "read1_passed": 12241194,
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                "properly paired_passed": 19760264,
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                "properly paired_failed_pct": NaN,
                "with itself and mate mapped_passed": 22556644,
                "with itself and mate mapped_failed": 0,
                "singletons_passed": 405040,
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                "singletons_passed_pct": 1.65,
                "singletons_failed_pct": NaN,
                "with mate mapped to a different chr_passed": 387138,
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                "with mate mapped to a different chr (mapQ >= 5)_passed": 146736,
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                "mapped_passed": 18514290,
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                "paired in sequencing_passed": 19563336,
                "paired in sequencing_failed": 0,
                "read1_passed": 9781668,
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                "properly paired_passed": 16047130,
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                "properly paired_failed_pct": NaN,
                "with itself and mate mapped_passed": 18156148,
                "with itself and mate mapped_failed": 0,
                "singletons_passed": 358142,
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                "singletons_passed_pct": 1.83,
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                "with mate mapped to a different chr_passed": 352816,
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                "with mate mapped to a different chr (mapQ >= 5)_passed": 130880,
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                "total_failed": 0,
                "duplicates_passed": 0,
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                "mapped_passed": 20230473,
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                "paired in sequencing_passed": 21068298,
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                "properly paired_passed": 15854766,
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                "properly paired_failed_pct": NaN,
                "with itself and mate mapped_passed": 19834272,
                "with itself and mate mapped_failed": 0,
                "singletons_passed": 396201,
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                "singletons_failed_pct": NaN,
                "with mate mapped to a different chr_passed": 450084,
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                "with mate mapped to a different chr (mapQ >= 5)_passed": 174121,
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                "flagstat_total": 21068298
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            "flagstat_G207M06": {
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                "total_failed": 0,
                "duplicates_passed": 0,
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                "mapped_passed": 18263103,
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                "paired in sequencing_passed": 19305508,
                "paired in sequencing_failed": 0,
                "read1_passed": 9652754,
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                "properly paired_passed": 15390370,
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                "with itself and mate mapped_passed": 17911754,
                "with itself and mate mapped_failed": 0,
                "singletons_passed": 351349,
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                "singletons_passed_pct": 1.82,
                "singletons_failed_pct": NaN,
                "with mate mapped to a different chr_passed": 346288,
                "with mate mapped to a different chr_failed": 0,
                "with mate mapped to a different chr (mapQ >= 5)_passed": 131059,
                "with mate mapped to a different chr (mapQ >= 5)_failed": 0,
                "flagstat_total": 19305508
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        },
        {
            "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
                "total_reads": 9781668,
                "paired_total": 9781668,
                "paired_aligned_none": 1758103,
                "paired_aligned_one": 3287307,
                "paired_aligned_multi": 4736258,
                "paired_aligned_discord_one": 648044,
                "paired_aligned_mate_none": 1049046,
                "paired_aligned_mate_one": 298605,
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                "overall_alignment_rate": 94.64,
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                "paired_aligned_mate_none_halved": 524523.0,
                "paired_aligned_mate_one_halved": 149302.5
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            "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
                "total_reads": 12241194,
                "paired_total": 12241194,
                "paired_aligned_none": 2361062,
                "paired_aligned_one": 4625132,
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                "paired_aligned_discord_one": 910202,
                "paired_aligned_mate_none": 1520704,
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                "overall_alignment_rate": 93.79,
                "paired_aligned_mate_multi_halved": 510162.5,
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            "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
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                "paired_aligned_none": 2606766,
                "paired_aligned_one": 4019341,
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                "overall_alignment_rate": 96.02,
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                "paired_aligned_mate_none_halved": 418912.5,
                "paired_aligned_mate_one_halved": 218060.5
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            "README_Bowtie2.sh": {
                "total_reads": 250000,
                "paired_total": 250000,
                "overall_alignment_rate": 95.16
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            "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
                "total_reads": 9652754,
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                "paired_aligned_none": 1957569,
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        {
            "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R2": {
                "percent_gc": 39.0,
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                "percent_duplicates": 35.922302809699346,
                "percent_fails": 9.090909090909092
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            "G207M5_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
                "percent_gc": 39.0,
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                "percent_duplicates": 36.93594145545368,
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            "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
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                "percent_duplicates": 35.10915606511395,
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            "G207M6_CKDL230025720-1A_HGLT2DSX7_L1_R2": {
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                "percent_duplicates": 34.08689929385234,
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            "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R2": {
                "percent_gc": 39.0,
                "avg_sequence_length": 150.0,
                "total_sequences": 10534149.0,
                "percent_duplicates": 29.09512548160737,
                "percent_fails": 9.090909090909092
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            "G207M7_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
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                "percent_duplicates": 30.382765133830503,
                "percent_fails": 9.090909090909092
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            "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R2": {
                "percent_gc": 39.0,
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                "total_sequences": 12241194.0,
                "percent_duplicates": 33.66230193603158,
                "percent_fails": 9.090909090909092
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            "G207M8_CKDL230025720-1A_HGLT2DSX7_L1_R1": {
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                "percent_duplicates": 34.86325334015292,
                "percent_fails": 9.090909090909092
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        }
    ],
    "report_general_stats_headers": [
        {
            "d": {
                "title": "Fragment Length",
                "min": 0,
                "format": "{:,.0f}",
                "namespace": "MACS2",
                "description": "Fragment Length",
                "rid": "mqc-generalstats-macs2-d",
                "scale": "GnBu",
                "colour": "55,126,184",
                "hidden": null,
                "max": null,
                "ceiling": null,
                "floor": null,
                "minRange": null,
                "shared_key": null,
                "modify": null,
                "placement": 1000.0,
                "dmax": 322.0,
                "dmin": 0.0
            },
            "peak_count": {
                "title": "Number of Peaks",
                "description": "Total number of peaks",
                "min": 0,
                "format": "{:,.0f}",
                "namespace": "MACS2",
                "rid": "mqc-generalstats-macs2-peak_count",
                "scale": "GnBu",
                "colour": "55,126,184",
                "hidden": null,
                "max": null,
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                "placement": 1000.0,
                "dmax": 8276.0,
                "dmin": 0.0
            }
        },
        {
            "summed_median": {
                "title": "Insert Size",
                "description": "Median Insert Size, all read orientations (bp)",
                "min": 0,
                "suffix": " bp",
                "format": "{:,.0f}",
                "scale": "GnBu",
                "namespace": "Picard",
                "rid": "mqc-generalstats-picard-summed_median",
                "colour": "77,175,74",
                "hidden": null,
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                "placement": 1000.0,
                "dmax": 319.0,
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            "summed_mean": {
                "title": "Mean Insert Size",
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                "format": "{:,.0f}",
                "scale": "GnBu",
                "hidden": true,
                "namespace": "Picard",
                "rid": "mqc-generalstats-picard-summed_mean",
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        {
            "flagstat_total": {
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                "modify": 1e-06,
                "shared_key": "read_count",
                "placement": 100.0,
                "hidden": true,
                "namespace": "Samtools",
                "rid": "mqc-generalstats-samtools-flagstat_total",
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            "mapped_passed": {
                "title": "M Reads Mapped",
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                "modify": 1e-06,
                "shared_key": "read_count",
                "placement": 101.0,
                "namespace": "Samtools",
                "rid": "mqc-generalstats-samtools-mapped_passed",
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        {
            "overall_alignment_rate": {
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                "description": "overall alignment rate",
                "max": 100,
                "min": 0,
                "suffix": "%",
                "scale": "YlGn",
                "namespace": "Bowtie 2 / HiSAT2",
                "rid": "mqc-generalstats-bowtie_2_hisat2-overall_alignment_rate",
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        {
            "percent_duplicates": {
                "title": "% Dups",
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                "max": 100,
                "min": 0,
                "suffix": "%",
                "scale": "RdYlGn-rev",
                "namespace": "FastQC",
                "rid": "mqc-generalstats-fastqc-percent_duplicates",
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            "percent_gc": {
                "title": "% GC",
                "description": "Average % GC Content",
                "max": 100,
                "min": 0,
                "suffix": "%",
                "scale": "Set1",
                "format": "{:,.0f}",
                "namespace": "FastQC",
                "rid": "mqc-generalstats-fastqc-percent_gc",
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            "avg_sequence_length": {
                "title": "Read Length",
                "description": "Average Read Length (bp)",
                "min": 0,
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                "scale": "RdYlGn",
                "format": "{:,.0f}",
                "hidden": true,
                "namespace": "FastQC",
                "rid": "mqc-generalstats-fastqc-avg_sequence_length",
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            "percent_fails": {
                "title": "% Failed",
                "description": "Percentage of modules failed in FastQC report (includes those not plotted here)",
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                "min": 0,
                "suffix": "%",
                "scale": "Reds",
                "format": "{:,.0f}",
                "hidden": true,
                "namespace": "FastQC",
                "rid": "mqc-generalstats-fastqc-percent_fails",
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            "total_sequences": {
                "title": "M Seqs",
                "description": "Total Sequences (millions)",
                "min": 0,
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                "modify": 1e-06,
                "shared_key": "read_count",
                "namespace": "FastQC",
                "rid": "mqc-generalstats-fastqc-total_sequences",
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