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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.14

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-08-14, 11:21 PDT based on data in: /home/shared/16TB_HDD_01/sam/gitrepos/RobertsLab/project-cod-temperature/output/14.00-heatwave-genetics-trimmed-bwa-alignments

        General Statistics

        Showing 344/344 rows and 8/11 columns.
        Sample Name% DupsError rateM Non-PrimaryM Reads Mapped% Mapped% Proper PairsM Total seqsM Reads Mapped
        MHW001-RG
        11.6%
        0.96%
        0.2
        21.1
        100.0%
        96.2%
        21.1
        21.2
        MHW002-RG
        9.9%
        0.93%
        0.2
        26.2
        100.0%
        96.4%
        26.2
        26.5
        MHW003-RG
        12.5%
        0.75%
        0.8
        63.1
        100.0%
        94.4%
        63.1
        63.9
        MHW004-RG
        10.2%
        0.70%
        1.1
        61.6
        100.0%
        94.5%
        61.6
        62.7
        MHW005-RG
        13.7%
        0.81%
        0.3
        29.6
        100.0%
        96.5%
        29.6
        29.9
        MHW006-RG
        9.5%
        1.02%
        0.4
        26.1
        100.0%
        94.3%
        26.1
        26.5
        MHW007-RG
        10.2%
        0.76%
        0.9
        51.5
        100.0%
        92.9%
        51.5
        52.4
        MHW008-RG
        10.7%
        0.74%
        1.0
        50.8
        100.0%
        90.6%
        50.8
        51.8
        MHW009-RG
        13.2%
        0.74%
        2.2
        73.2
        100.0%
        88.0%
        73.2
        75.5
        MHW010-RG
        13.9%
        0.74%
        6.0
        79.8
        100.0%
        75.2%
        79.8
        85.9
        MHW011-RG
        12.6%
        0.76%
        4.7
        73.5
        100.0%
        81.9%
        73.5
        78.2
        MHW012-RG
        12.0%
        0.73%
        7.1
        88.8
        100.0%
        81.1%
        88.8
        96.0
        MHW013-RG
        14.8%
        0.76%
        5.6
        83.3
        100.0%
        70.3%
        83.3
        88.9
        MHW014-RG
        11.4%
        0.70%
        12.7
        72.4
        100.0%
        65.0%
        72.4
        85.1
        MHW015-RG
        12.6%
        6.89%
        5.7
        63.9
        100.0%
        75.4%
        63.9
        69.6
        MHW016-RG
        12.7%
        0.74%
        4.5
        81.7
        100.0%
        80.0%
        81.7
        86.2
        MHW017-RG
        11.7%
        0.67%
        16.2
        78.9
        100.0%
        64.4%
        78.9
        95.1
        MHW018-RG
        16.2%
        1.33%
        0.8
        71.5
        100.0%
        96.1%
        71.5
        72.3
        MHW019-RG
        9.9%
        1.02%
        0.9
        57.4
        100.0%
        96.4%
        57.4
        58.3
        MHW020-RG
        13.0%
        1.18%
        0.7
        59.7
        100.0%
        96.5%
        59.7
        60.5
        MHW021-RG
        9.4%
        1.09%
        1.0
        60.2
        100.0%
        95.8%
        60.2
        61.2
        MHW022-RG
        11.8%
        1.19%
        0.7
        52.2
        100.0%
        95.6%
        52.2
        52.9
        MHW023-RG
        6.7%
        1.08%
        2.1
        49.3
        100.0%
        93.5%
        49.3
        51.3
        MHW024-RG
        20.2%
        1.18%
        1.0
        101.9
        100.0%
        95.7%
        101.9
        102.9
        MHW025-RG
        17.3%
        1.13%
        1.1
        101.1
        100.0%
        96.1%
        101.1
        102.2
        MHW026-RG
        13.2%
        1.15%
        0.9
        77.5
        100.0%
        95.6%
        77.5
        78.3
        MHW027-RG
        16.7%
        0.96%
        1.0
        109.0
        100.0%
        96.9%
        109.0
        110.0
        MHW028-RG
        14.3%
        1.13%
        0.7
        71.0
        100.0%
        95.9%
        71.0
        71.7
        MHW029-RG
        16.3%
        1.01%
        0.8
        88.2
        100.0%
        96.3%
        88.2
        89.0
        MHW030-RG
        12.3%
        1.15%
        0.5
        42.6
        100.0%
        95.4%
        42.6
        43.0
        MHW031-RG
        19.6%
        1.17%
        1.0
        88.6
        100.0%
        95.4%
        88.6
        89.6
        MHW032-RG
        14.5%
        0.75%
        2.0
        79.7
        100.0%
        86.5%
        79.7
        81.6
        MHW033-RG
        13.2%
        0.76%
        1.4
        77.2
        100.0%
        90.8%
        77.2
        78.6
        MHW034-RG
        12.9%
        0.76%
        2.4
        78.3
        100.0%
        87.3%
        78.3
        80.7
        MHW035-RG
        14.5%
        0.75%
        2.0
        85.5
        100.0%
        88.7%
        85.5
        87.4
        MHW036-RG
        14.4%
        3.19%
        4.0
        76.6
        100.0%
        83.8%
        76.6
        80.6
        MHW037-RG
        13.1%
        0.75%
        1.6
        75.8
        100.0%
        89.8%
        75.8
        77.4
        MHW038-RG
        12.8%
        0.76%
        2.3
        81.7
        100.0%
        88.0%
        81.7
        83.9
        MHW039-RG
        24.6%
        0.72%
        1.1
        107.3
        100.0%
        94.2%
        107.3
        108.4
        MHW040-RG
        20.2%
        0.73%
        1.2
        106.1
        100.0%
        95.2%
        106.1
        107.2
        MHW041-RG
        20.6%
        0.74%
        1.1
        93.1
        100.0%
        95.1%
        93.1
        94.2
        MHW042-RG
        23.4%
        0.71%
        1.0
        102.9
        100.0%
        95.0%
        102.9
        103.9
        MHW043-RG
        22.7%
        0.72%
        1.1
        101.1
        100.0%
        94.8%
        101.1
        102.2
        MHW044-RG
        18.1%
        0.74%
        1.1
        95.2
        100.0%
        95.2%
        95.2
        96.3
        MHW045-RG
        17.9%
        0.73%
        0.9
        83.6
        100.0%
        95.5%
        83.6
        84.6
        MHW046-RG
        22.0%
        0.73%
        1.1
        100.7
        100.0%
        94.8%
        100.7
        101.8
        MHW047-RG
        12.8%
        0.76%
        1.7
        97.6
        100.0%
        93.0%
        97.6
        99.3
        MHW048-RG
        11.8%
        0.76%
        1.5
        91.1
        100.0%
        93.3%
        91.1
        92.6
        MHW049-RG
        12.8%
        0.76%
        1.3
        83.1
        100.0%
        93.8%
        83.1
        84.3
        MHW050-RG
        13.2%
        0.75%
        1.5
        80.8
        100.0%
        92.0%
        80.8
        82.3
        MHW051-RG
        13.3%
        0.74%
        2.6
        95.8
        100.0%
        85.8%
        95.8
        98.5
        MHW052-RG
        14.3%
        0.74%
        1.5
        91.0
        100.0%
        91.6%
        91.0
        92.5
        MHW053-RG
        13.1%
        0.76%
        1.5
        92.8
        100.0%
        92.6%
        92.8
        94.3
        MHW054-RG
        15.0%
        0.75%
        1.3
        99.0
        100.0%
        94.0%
        99.0
        100.3
        MHW055-RG
        11.6%
        0.74%
        1.2
        88.7
        100.0%
        94.5%
        88.7
        89.9
        MHW056-RG
        13.1%
        0.74%
        1.6
        98.0
        100.0%
        90.8%
        98.0
        99.6
        MHW057-RG
        12.3%
        0.73%
        1.3
        91.5
        100.0%
        92.7%
        91.5
        92.8
        MHW058-RG
        13.1%
        0.73%
        1.9
        93.4
        100.0%
        88.5%
        93.4
        95.2
        MHW059-RG
        12.6%
        0.75%
        2.7
        97.9
        100.0%
        85.3%
        97.9
        100.6
        MHW060-RG
        13.2%
        0.75%
        1.3
        96.1
        100.0%
        93.0%
        96.1
        97.4
        MHW061-RG
        13.1%
        0.74%
        2.1
        95.2
        100.0%
        87.2%
        95.2
        97.3
        MHW062-RG
        12.7%
        0.74%
        1.8
        102.1
        100.0%
        90.8%
        102.1
        103.9
        MHW063-RG
        12.9%
        0.75%
        1.7
        94.1
        100.0%
        90.3%
        94.1
        95.7
        MHW064-RG
        11.8%
        0.75%
        1.4
        94.5
        100.0%
        92.5%
        94.5
        95.9
        MHW065-RG
        12.8%
        0.75%
        1.3
        100.1
        100.0%
        93.9%
        100.1
        101.4
        MHW066-RG
        13.5%
        0.74%
        2.0
        93.9
        100.0%
        87.9%
        93.9
        95.9
        MHW067-RG
        14.9%
        0.74%
        2.0
        86.1
        100.0%
        84.8%
        86.1
        88.1
        MHW068-RG
        13.5%
        0.76%
        1.4
        84.0
        100.0%
        91.3%
        84.0
        85.4
        MHW069-RG
        13.7%
        0.76%
        1.3
        72.6
        100.0%
        89.4%
        72.6
        74.0
        MHW070-RG
        12.4%
        0.77%
        1.4
        66.7
        100.0%
        88.7%
        66.7
        68.1
        MHW071-RG
        13.2%
        6.93%
        4.3
        64.2
        100.0%
        83.3%
        64.2
        68.5
        MHW072-RG
        14.9%
        0.74%
        2.2
        73.0
        100.0%
        80.5%
        73.0
        75.2
        MHW073-RG
        13.8%
        0.74%
        1.0
        64.7
        100.0%
        92.3%
        64.7
        65.7
        MHW074-RG
        15.5%
        0.74%
        1.7
        88.2
        100.0%
        89.0%
        88.2
        89.8
        MHW075-RG
        15.3%
        0.73%
        1.0
        67.0
        100.0%
        92.0%
        67.0
        68.0
        MHW076-RG
        14.5%
        0.73%
        1.4
        78.7
        100.0%
        90.8%
        78.7
        80.1
        MHW077-RG
        12.6%
        0.75%
        1.0
        66.9
        100.0%
        92.9%
        66.9
        67.9
        MHW078-RG
        12.9%
        0.73%
        1.0
        65.6
        100.0%
        91.7%
        65.6
        66.6
        MHW079-RG
        15.1%
        0.74%
        1.7
        78.5
        100.0%
        86.6%
        78.5
        80.2
        MHW080-RG
        15.1%
        0.74%
        1.5
        67.0
        100.0%
        87.2%
        67.0
        68.6
        MHW081-RG
        12.0%
        0.73%
        2.0
        67.1
        100.0%
        86.9%
        67.1
        69.0
        MHW082-RG
        13.9%
        0.75%
        1.6
        73.1
        100.0%
        87.9%
        73.1
        74.8
        MHW083-RG
        13.4%
        0.73%
        1.5
        73.3
        100.0%
        90.2%
        73.3
        74.8
        MHW084-RG
        14.2%
        0.74%
        1.9
        78.4
        100.0%
        86.8%
        78.4
        80.3
        MHW085-RG
        11.7%
        0.76%
        1.1
        65.5
        100.0%
        92.7%
        65.5
        66.6
        MHW086-RG
        12.4%
        0.73%
        1.8
        69.9
        100.0%
        85.0%
        69.9
        71.7
        MHW087-RG
        12.8%
        0.74%
        2.9
        84.5
        100.0%
        84.2%
        84.5
        87.3
        MHW088-RG
        14.8%
        0.71%
        3.0
        75.5
        100.0%
        78.3%
        75.5
        78.5
        MHW089-RG
        12.9%
        0.75%
        4.3
        73.3
        100.0%
        76.4%
        73.3
        77.6
        MHW090-RG
        13.1%
        0.75%
        2.8
        66.4
        100.0%
        82.4%
        66.4
        69.1
        MHW091-RG
        12.9%
        0.78%
        0.9
        66.1
        100.0%
        95.6%
        66.1
        67.0
        MHW092-RG
        13.1%
        0.80%
        1.1
        67.4
        100.0%
        94.8%
        67.4
        68.4
        MHW093-RG
        12.1%
        0.85%
        1.3
        77.4
        100.0%
        94.8%
        77.4
        78.7
        MHW094-RG
        13.0%
        0.85%
        1.5
        82.5
        100.0%
        94.2%
        82.5
        84.0
        MHW095-RG
        13.1%
        0.81%
        1.4
        82.8
        100.0%
        95.0%
        82.8
        84.1
        MHW096-RG
        15.0%
        0.78%
        1.4
        98.5
        100.0%
        95.5%
        98.5
        99.8
        MHW097-RG
        9.8%
        0.89%
        3.9
        66.1
        100.0%
        85.8%
        66.1
        70.0
        MHW098-RG
        7.6%
        0.81%
        9.5
        59.5
        100.0%
        74.8%
        59.5
        69.0
        MHW099-RG
        7.6%
        0.81%
        6.5
        63.7
        100.0%
        79.9%
        63.7
        70.2
        MHW100-RG
        8.2%
        0.84%
        8.6
        68.3
        100.0%
        78.9%
        68.3
        76.9
        MHW101-RG
        8.0%
        0.79%
        9.6
        66.5
        100.0%
        72.2%
        66.5
        76.1
        MHW102-RG
        8.9%
        0.80%
        10.9
        73.7
        100.0%
        74.2%
        73.7
        84.6
        MHW103-RG
        10.2%
        0.75%
        7.4
        64.0
        100.0%
        69.6%
        64.0
        71.4
        MHW104-RG
        8.0%
        0.79%
        5.1
        61.7
        100.0%
        81.5%
        61.7
        66.8
        MHW105-RG
        9.1%
        0.78%
        2.9
        65.2
        100.0%
        86.8%
        65.2
        68.1
        MHW106-RG
        11.5%
        0.73%
        10.5
        65.4
        100.0%
        57.0%
        65.4
        75.9
        MHW107-RG
        10.3%
        0.76%
        2.3
        64.6
        100.0%
        88.6%
        64.6
        66.9
        MHW108-RG
        8.8%
        0.79%
        5.0
        69.4
        100.0%
        83.6%
        69.4
        74.4
        MHW109-RG
        9.3%
        0.79%
        3.9
        65.4
        100.0%
        84.2%
        65.4
        69.3
        MHW110-RG
        9.7%
        0.83%
        4.6
        74.7
        100.0%
        87.3%
        74.7
        79.4
        MHW111-RG
        11.2%
        0.76%
        2.2
        69.6
        100.0%
        87.8%
        69.6
        71.8
        MHW112-RG
        9.3%
        0.78%
        2.9
        57.2
        100.0%
        85.0%
        57.2
        60.0
        MHW113-RG
        9.7%
        0.83%
        2.8
        62.8
        100.0%
        88.4%
        62.8
        65.6
        MHW114-RG
        9.6%
        0.76%
        15.0
        64.6
        100.0%
        61.2%
        64.6
        79.7
        MHW115-RG
        10.7%
        0.78%
        2.3
        97.8
        100.0%
        93.0%
        97.8
        100.0
        MHW116-RG
        9.8%
        0.79%
        1.5
        69.1
        100.0%
        92.6%
        69.1
        70.5
        MHW117-RG
        9.4%
        0.81%
        2.2
        74.9
        100.0%
        91.2%
        74.9
        77.2
        MHW118-RG
        9.3%
        0.82%
        2.8
        68.0
        100.0%
        88.6%
        68.0
        70.9
        MHW119-RG
        11.6%
        0.80%
        2.2
        79.6
        100.0%
        90.5%
        79.6
        81.8
        MHW120-RG
        13.0%
        0.84%
        1.3
        81.1
        100.0%
        94.7%
        81.1
        82.5
        MHW121-RG
        16.3%
        0.77%
        1.4
        101.2
        100.0%
        95.0%
        101.2
        102.6
        MHW122-RG
        13.3%
        0.78%
        1.2
        84.2
        100.0%
        95.5%
        84.2
        85.4
        MHW123-RG
        16.5%
        0.78%
        1.4
        92.5
        100.0%
        94.7%
        92.5
        93.8
        MHW124-RG
        12.6%
        0.87%
        1.8
        91.5
        100.0%
        94.3%
        91.5
        93.2
        MHW125-RG
        14.4%
        0.75%
        1.1
        86.2
        100.0%
        95.7%
        86.2
        87.3
        MHW126-RG
        13.2%
        0.91%
        1.3
        74.2
        100.0%
        94.8%
        74.2
        75.5
        MHW127-RG
        13.6%
        0.84%
        1.5
        85.2
        100.0%
        94.0%
        85.2
        86.7
        MHW128-RG
        15.5%
        0.76%
        1.3
        96.3
        100.0%
        95.5%
        96.3
        97.6
        MHW129-RG
        17.9%
        0.76%
        1.5
        114.5
        100.0%
        95.4%
        114.5
        116.0
        MHW130-RG
        14.7%
        0.87%
        1.6
        91.7
        100.0%
        94.3%
        91.7
        93.3
        MHW131-RG
        16.4%
        0.84%
        1.9
        107.9
        100.0%
        94.6%
        107.9
        109.8
        MHW132-RG
        14.6%
        0.83%
        1.4
        88.2
        100.0%
        94.9%
        88.2
        89.7
        MHW133-RG
        15.5%
        0.79%
        1.4
        97.0
        100.0%
        95.0%
        97.0
        98.4
        MHW134-RG
        13.5%
        0.76%
        1.0
        79.3
        100.0%
        95.7%
        79.3
        80.3
        MHW135-RG
        17.0%
        0.81%
        1.6
        92.8
        100.0%
        94.4%
        92.8
        94.4
        MHW136-RG
        12.3%
        0.78%
        1.4
        91.0
        100.0%
        93.0%
        91.0
        92.4
        MHW137-RG
        11.8%
        0.76%
        1.7
        96.4
        100.0%
        91.8%
        96.4
        98.1
        MHW138-RG
        11.9%
        0.74%
        1.8
        108.0
        100.0%
        91.9%
        108.0
        109.8
        MHW139-RG
        11.9%
        0.75%
        2.9
        99.1
        100.0%
        87.1%
        99.1
        102.0
        MHW140-RG
        15.2%
        0.73%
        2.6
        86.3
        100.0%
        82.6%
        86.3
        88.9
        MHW141-RG
        14.3%
        0.75%
        1.6
        88.4
        100.0%
        90.5%
        88.4
        90.0
        MHW142-RG
        14.5%
        0.75%
        2.1
        90.0
        100.0%
        87.4%
        90.0
        92.1
        MHW143-RG
        13.7%
        0.74%
        2.2
        99.0
        100.0%
        90.2%
        99.0
        101.2
        MHW144-RG
        13.0%
        0.75%
        1.7
        84.3
        100.0%
        90.0%
        84.3
        86.0
        MHW145-RG
        13.9%
        0.75%
        3.6
        93.0
        100.0%
        79.9%
        93.0
        96.6
        MHW146-RG
        12.6%
        0.77%
        2.1
        86.6
        100.0%
        90.8%
        86.6
        88.6
        MHW147-RG
        12.9%
        0.74%
        5.5
        88.0
        100.0%
        78.8%
        88.0
        93.5
        MHW148-RG
        13.5%
        0.74%
        5.8
        98.9
        100.0%
        79.8%
        98.9
        104.6
        MHW149-RG
        15.8%
        3.14%
        5.6
        103.0
        100.0%
        84.6%
        103.0
        108.7
        MHW150-RG
        13.5%
        0.77%
        3.0
        100.2
        100.0%
        89.4%
        100.2
        103.2
        MHW151-RG
        14.8%
        0.74%
        3.6
        107.0
        100.0%
        86.7%
        107.0
        110.6
        MHW152-RG
        13.0%
        0.76%
        2.2
        96.2
        100.0%
        91.5%
        96.2
        98.3
        MHW153-RG
        12.6%
        0.76%
        3.3
        100.3
        100.0%
        88.6%
        100.3
        103.6
        MHW154-RG
        13.4%
        0.77%
        1.9
        89.7
        100.0%
        92.2%
        89.7
        91.6
        MHW155-RG
        14.7%
        0.74%
        8.2
        101.5
        100.0%
        75.8%
        101.5
        109.7
        MHW156-RG
        22.1%
        0.73%
        0.9
        81.6
        100.0%
        95.2%
        81.6
        82.5
        MHW157-RG
        21.0%
        0.72%
        1.0
        91.5
        100.0%
        95.5%
        91.5
        92.5
        MHW158-RG
        19.8%
        0.74%
        1.3
        105.5
        100.0%
        95.8%
        105.5
        106.8
        MHW159-RG
        16.5%
        0.75%
        1.0
        80.9
        100.0%
        96.1%
        80.9
        81.8
        MHW160-RG
        19.6%
        0.73%
        1.0
        83.4
        100.0%
        95.5%
        83.4
        84.4
        MHW161-RG
        18.6%
        0.74%
        1.0
        82.7
        100.0%
        95.5%
        82.7
        83.7
        MHW162-RG
        19.2%
        0.72%
        0.9
        83.6
        100.0%
        95.7%
        83.6
        84.5
        MHW163-RG
        17.7%
        0.75%
        1.0
        84.6
        100.0%
        95.5%
        84.6
        85.6
        MHW164-RG
        17.0%
        0.75%
        1.0
        78.8
        100.0%
        95.6%
        78.8
        79.8
        MHW165-RG
        17.4%
        0.72%
        1.0
        88.7
        100.0%
        95.8%
        88.7
        89.6
        MHW166-RG
        20.5%
        0.75%
        1.1
        94.8
        100.0%
        95.2%
        94.8
        95.9
        MHW167-RG
        17.2%
        0.74%
        1.0
        85.3
        100.0%
        95.8%
        85.3
        86.2
        MHW168-RG
        18.3%
        0.72%
        0.9
        82.7
        100.0%
        95.6%
        82.7
        83.6
        MHW169-RG
        16.3%
        0.73%
        0.9
        80.1
        100.0%
        95.8%
        80.1
        81.0
        MHW170-RG
        14.9%
        0.73%
        1.0
        86.8
        100.0%
        96.2%
        86.8
        87.8
        MHW171-RG
        18.4%
        0.74%
        1.3
        113.8
        100.0%
        95.4%
        113.8
        115.1
        MHW172-RG
        17.9%
        0.75%
        1.0
        80.3
        100.0%
        95.5%
        80.3
        81.3
        MHW173-RG
        19.2%
        0.73%
        0.9
        83.4
        100.0%
        95.4%
        83.4
        84.3
        MHW174-RG
        18.9%
        0.73%
        1.0
        89.9
        100.0%
        95.6%
        89.9
        90.9
        MHW175-RG
        15.4%
        0.74%
        0.9
        79.0
        100.0%
        95.9%
        79.0
        79.9
        MHW176-RG
        8.8%
        0.75%
        8.5
        72.1
        100.0%
        76.4%
        72.1
        80.6
        MHW177-RG
        11.1%
        0.77%
        2.6
        63.8
        100.0%
        86.3%
        63.8
        66.3
        MHW178-RG
        10.6%
        0.77%
        1.8
        58.9
        100.0%
        89.4%
        58.9
        60.7
        MHW179-RG
        11.7%
        0.78%
        2.3
        61.8
        100.0%
        86.6%
        61.8
        64.0
        MHW180-RG
        12.7%
        0.76%
        4.0
        65.1
        100.0%
        79.3%
        65.1
        69.2
        MHW181-RG
        11.4%
        0.72%
        4.1
        58.0
        100.0%
        81.5%
        58.0
        62.1
        MHW182-RG
        12.6%
        0.76%
        1.7
        71.4
        100.0%
        91.2%
        71.4
        73.0
        MHW183-RG
        13.5%
        0.74%
        4.3
        70.8
        100.0%
        81.8%
        70.8
        75.1
        MHW184-RG
        13.0%
        0.73%
        4.0
        69.6
        100.0%
        82.1%
        69.6
        73.6
        MHW185-RG
        10.9%
        0.74%
        1.6
        60.0
        100.0%
        91.3%
        60.0
        61.6
        MHW186-RG
        21.4%
        0.73%
        1.0
        91.1
        100.0%
        95.1%
        91.1
        92.1
        MHW187-RG
        21.0%
        0.71%
        1.1
        96.7
        100.0%
        95.1%
        96.7
        97.9
        MHW188-RG
        21.5%
        0.72%
        1.1
        92.8
        100.0%
        95.1%
        92.8
        93.9
        MHW189-RG
        23.0%
        0.72%
        1.1
        100.2
        100.0%
        94.9%
        100.2
        101.4
        MHW190-RG
        17.9%
        0.72%
        1.0
        83.4
        100.0%
        95.6%
        83.4
        84.4
        MHW191-RG
        20.8%
        0.73%
        1.0
        88.0
        100.0%
        94.9%
        88.0
        89.0
        MHW192-RG
        16.5%
        0.73%
        0.9
        68.7
        100.0%
        95.7%
        68.7
        69.6
        MHW193-RG
        19.4%
        0.71%
        1.0
        88.0
        100.0%
        95.4%
        88.0
        89.1
        MHW194-RG
        16.2%
        0.73%
        0.9
        83.1
        100.0%
        95.7%
        83.1
        84.0
        MHW195-RG
        17.5%
        0.74%
        1.0
        88.5
        100.0%
        95.4%
        88.5
        89.6
        MHW196-RG
        6.9%
        0.74%
        1.8
        55.3
        100.0%
        94.1%
        55.3
        57.1
        MHW197-RG
        6.5%
        0.73%
        11.1
        66.3
        100.0%
        81.6%
        66.3
        77.4
        MHW198-RG
        11.3%
        0.79%
        2.4
        68.5
        100.0%
        94.7%
        68.5
        70.9
        MHW199-RG
        7.7%
        0.71%
        5.5
        70.4
        100.0%
        88.2%
        70.4
        76.0
        MHW200-RG
        13.0%
        0.71%
        7.6
        71.5
        100.0%
        72.2%
        71.5
        79.1
        MHW201-RG
        7.7%
        0.73%
        2.9
        64.8
        100.0%
        93.3%
        64.8
        67.7
        MHW202-RG
        7.6%
        0.73%
        9.0
        81.6
        100.0%
        88.5%
        81.6
        90.6
        MHW203-RG
        7.8%
        0.66%
        16.2
        61.5
        100.0%
        68.2%
        61.5
        77.8
        MHW204-RG
        7.2%
        0.72%
        6.6
        60.3
        100.0%
        87.8%
        60.3
        66.9
        MHW205-RG
        9.5%
        0.76%
        1.2
        58.7
        100.0%
        96.4%
        58.7
        59.9
        MHW206-RG
        11.8%
        0.89%
        0.5
        36.6
        100.0%
        96.8%
        36.6
        37.1
        MHW207-RG
        9.5%
        0.88%
        0.6
        57.5
        100.0%
        97.1%
        57.5
        58.1
        MHW208-RG
        11.3%
        0.73%
        2.3
        78.0
        100.0%
        90.4%
        78.0
        80.3
        MHW209-RG
        14.1%
        0.75%
        3.3
        68.6
        100.0%
        82.2%
        68.6
        71.9
        MHW210-RG
        14.3%
        0.74%
        1.4
        77.9
        100.0%
        91.8%
        77.9
        79.3
        MHW211-RG
        13.9%
        0.75%
        2.6
        71.7
        100.0%
        85.1%
        71.7
        74.3
        MHW212-RG
        12.2%
        0.74%
        4.6
        66.5
        100.0%
        78.7%
        66.5
        71.1
        MHW213-RG
        11.8%
        0.75%
        3.4
        74.1
        100.0%
        85.8%
        74.1
        77.5
        MHW214-RG
        12.8%
        0.77%
        1.0
        75.8
        100.0%
        94.4%
        75.8
        76.9
        MHW215-RG
        14.9%
        0.74%
        1.8
        91.0
        100.0%
        91.2%
        91.0
        92.8
        MHW216-RG
        14.9%
        0.75%
        2.7
        72.8
        100.0%
        84.4%
        72.8
        75.4
        MHW217-RG
        16.1%
        0.73%
        3.2
        90.4
        100.0%
        83.5%
        90.4
        93.6
        MHW218-RG
        13.9%
        0.76%
        1.4
        71.6
        100.0%
        91.7%
        71.6
        73.0
        MHW219-RG
        21.3%
        0.72%
        1.0
        92.1
        100.0%
        95.0%
        92.1
        93.1
        MHW220-RG
        18.7%
        0.72%
        1.0
        91.2
        100.0%
        95.5%
        91.2
        92.2
        MHW221-RG
        18.5%
        0.74%
        1.0
        84.0
        100.0%
        95.3%
        84.0
        84.9
        MHW222-RG
        18.2%
        0.74%
        1.1
        93.0
        100.0%
        95.1%
        93.0
        94.1
        MHW223-RG
        18.3%
        0.75%
        0.9
        76.4
        100.0%
        95.0%
        76.4
        77.4
        MHW224-RG
        20.4%
        0.75%
        1.1
        93.6
        100.0%
        94.7%
        93.6
        94.8
        MHW225-RG
        20.6%
        0.71%
        1.1
        107.0
        100.0%
        95.4%
        107.0
        108.1
        MHW226-RG
        22.3%
        0.72%
        1.1
        104.7
        100.0%
        95.0%
        104.7
        105.8
        MHW227-RG
        21.0%
        0.74%
        1.3
        106.3
        100.0%
        95.2%
        106.3
        107.6
        MHW228-RG
        20.1%
        0.73%
        1.2
        104.9
        100.0%
        95.6%
        104.9
        106.1
        MHW229-RG
        18.0%
        0.73%
        1.2
        100.8
        100.0%
        95.5%
        100.8
        102.0
        MHW230-RG
        20.1%
        0.73%
        1.2
        102.0
        100.0%
        95.0%
        102.0
        103.2
        MHW231-RG
        17.5%
        0.73%
        1.0
        87.9
        100.0%
        95.6%
        87.9
        88.9
        MHW232-RG
        18.3%
        0.72%
        1.1
        98.0
        100.0%
        95.6%
        98.0
        99.1
        MHW233-RG
        16.9%
        0.73%
        1.1
        90.6
        100.0%
        95.2%
        90.6
        91.7
        MHW234-RG
        16.5%
        0.76%
        1.2
        100.9
        100.0%
        95.3%
        100.9
        102.1
        MHW235-RG
        19.1%
        0.74%
        1.1
        87.9
        100.0%
        94.8%
        87.9
        89.0
        MHW236-RG
        17.7%
        0.72%
        1.3
        99.2
        100.0%
        95.1%
        99.2
        100.5
        MHW237-RG
        17.5%
        0.72%
        1.0
        91.2
        100.0%
        95.3%
        91.2
        92.3
        MHW238-RG
        17.8%
        0.73%
        1.2
        92.4
        100.0%
        94.8%
        92.4
        93.5
        MHW239-RG
        17.4%
        0.76%
        0.9
        67.0
        100.0%
        95.0%
        67.0
        67.9
        MHW240-RG
        20.4%
        0.74%
        1.0
        89.0
        100.0%
        95.0%
        89.0
        90.0
        MHW241-RG
        18.6%
        0.73%
        1.0
        87.9
        100.0%
        95.2%
        87.9
        88.9
        MHW258-RG
        16.4%
        0.73%
        0.9
        81.4
        100.0%
        95.8%
        81.4
        82.3
        MHW260-RG
        16.8%
        0.76%
        1.1
        88.7
        100.0%
        95.2%
        88.7
        89.8
        MHW263-RG
        15.1%
        0.74%
        0.9
        80.0
        100.0%
        95.8%
        80.0
        80.9
        MHW265-RG
        14.8%
        0.79%
        1.1
        80.8
        100.0%
        95.3%
        80.8
        81.9
        MHW267-RG
        17.4%
        0.76%
        1.0
        78.4
        100.0%
        95.2%
        78.4
        79.3
        MHW268-RG
        19.0%
        0.74%
        1.1
        96.9
        100.0%
        95.3%
        96.9
        98.0
        MHW269-RG
        14.7%
        0.76%
        1.0
        76.4
        100.0%
        95.5%
        76.4
        77.3
        MHW270-RG
        13.9%
        0.77%
        0.9
        76.8
        100.0%
        95.7%
        76.8
        77.7
        MHW271-RG
        13.9%
        0.74%
        0.8
        67.2
        100.0%
        96.1%
        67.2
        68.0
        MHW272-RG
        14.3%
        0.76%
        1.0
        76.3
        100.0%
        95.5%
        76.3
        77.3
        MHW273-RG
        19.5%
        0.72%
        0.9
        87.5
        100.0%
        95.2%
        87.5
        88.4
        MHW274-RG
        17.9%
        0.72%
        1.0
        88.0
        100.0%
        95.6%
        88.0
        89.0
        MHW275-RG
        18.8%
        0.74%
        1.0
        83.0
        100.0%
        95.3%
        83.0
        84.0
        MHW276-RG
        16.2%
        0.77%
        1.0
        82.4
        100.0%
        95.6%
        82.4
        83.4
        MHW277-RG
        18.7%
        0.72%
        0.9
        86.3
        100.0%
        95.4%
        86.3
        87.2
        MHW278-RG
        16.0%
        0.72%
        0.9
        80.6
        100.0%
        95.6%
        80.6
        81.5
        MHW279-RG
        15.1%
        0.76%
        0.8
        66.8
        100.0%
        95.5%
        66.8
        67.5
        MHW280-RG
        18.2%
        0.72%
        0.9
        84.7
        100.0%
        95.6%
        84.7
        85.6
        MHW281-RG
        20.9%
        0.72%
        1.0
        90.8
        100.0%
        95.3%
        90.8
        91.8
        MHW282-RG
        17.4%
        0.74%
        1.1
        90.6
        100.0%
        95.7%
        90.6
        91.6
        MHW283-RG
        19.4%
        0.75%
        1.1
        88.9
        100.0%
        95.3%
        88.9
        90.0
        MHW284-RG
        18.1%
        0.72%
        0.9
        84.5
        100.0%
        95.6%
        84.5
        85.4
        MHW285-RG
        19.0%
        0.72%
        0.9
        84.0
        100.0%
        95.4%
        84.0
        84.9
        MHW286-RG
        20.1%
        0.74%
        1.0
        87.1
        100.0%
        95.1%
        87.1
        88.1
        MHW287-RG
        17.4%
        0.73%
        0.8
        73.9
        100.0%
        95.7%
        73.9
        74.7
        MHW288-RG
        17.4%
        0.75%
        1.0
        87.1
        100.0%
        95.5%
        87.1
        88.1
        MHW289-RG
        15.4%
        0.74%
        1.2
        76.0
        100.0%
        91.1%
        76.0
        77.2
        MHW290-RG
        16.0%
        0.74%
        1.4
        80.0
        100.0%
        90.0%
        80.0
        81.3
        MHW291-RG
        16.1%
        0.74%
        1.4
        68.5
        100.0%
        87.6%
        68.5
        69.9
        MHW292-RG
        15.2%
        0.74%
        1.3
        93.7
        100.0%
        92.6%
        93.7
        95.0
        MHW293-RG
        15.5%
        0.74%
        1.6
        91.5
        100.0%
        89.6%
        91.5
        93.1
        MHW294-RG
        15.6%
        0.75%
        1.5
        96.8
        100.0%
        91.0%
        96.8
        98.3
        MHW295-RG
        16.6%
        0.74%
        1.5
        102.2
        100.0%
        92.6%
        102.2
        103.6
        MHW296-RG
        16.1%
        0.74%
        2.6
        112.3
        100.0%
        84.8%
        112.3
        114.9
        MHW297-RG
        15.6%
        3.16%
        4.6
        97.8
        100.0%
        86.1%
        97.8
        102.4
        MHW298-RG
        14.9%
        0.77%
        1.4
        97.9
        100.0%
        93.2%
        97.9
        99.3
        MHW299-RG
        15.5%
        0.75%
        2.0
        89.1
        100.0%
        86.1%
        89.1
        91.1
        MHW300-RG
        16.2%
        0.74%
        1.9
        105.5
        100.0%
        89.2%
        105.5
        107.4
        MHW301-RG
        15.8%
        0.77%
        1.8
        102.6
        100.0%
        90.2%
        102.6
        104.4
        MHW302-RG
        15.0%
        0.77%
        1.3
        95.7
        100.0%
        94.0%
        95.7
        96.9
        MHW303-RG
        15.2%
        0.75%
        1.3
        102.8
        100.0%
        94.5%
        102.8
        104.0
        MHW304-RG
        14.5%
        7.19%
        6.3
        94.4
        100.0%
        85.4%
        94.4
        100.7
        MHW305-RG
        14.0%
        0.76%
        1.2
        95.7
        100.0%
        94.4%
        95.7
        96.8
        MHW306-RG
        14.6%
        0.77%
        1.2
        94.3
        100.0%
        94.0%
        94.3
        95.5
        MHW307-RG
        14.6%
        0.75%
        1.5
        108.6
        100.0%
        93.0%
        108.6
        110.1
        MHW308-RG
        14.9%
        0.72%
        1.2
        81.8
        100.0%
        92.0%
        81.8
        83.0
        MHW309-RG
        15.9%
        0.75%
        1.4
        89.1
        100.0%
        91.3%
        89.1
        90.5
        MHW310-RG
        15.6%
        0.74%
        1.1
        88.3
        100.0%
        93.6%
        88.3
        89.5
        MHW311-RG
        24.0%
        0.82%
        1.0
        71.2
        100.0%
        95.3%
        71.2
        72.1
        MHW312-RG
        22.6%
        0.71%
        1.1
        111.5
        100.0%
        94.9%
        111.5
        112.6
        MHW313-RG
        21.3%
        0.73%
        1.0
        90.2
        100.0%
        94.9%
        90.2
        91.2
        MHW314-RG
        22.0%
        0.74%
        1.0
        89.5
        100.0%
        94.9%
        89.5
        90.5
        MHW315-RG
        18.4%
        0.72%
        0.9
        83.9
        100.0%
        95.3%
        83.9
        84.8
        MHW316-RG
        20.0%
        0.70%
        0.8
        81.4
        100.0%
        95.5%
        81.4
        82.1
        MHW317-RG
        19.6%
        0.74%
        0.9
        78.4
        100.0%
        95.1%
        78.4
        79.3
        MHW318-RG
        20.6%
        0.71%
        0.8
        84.3
        100.0%
        95.4%
        84.3
        85.2
        MHW319-RG
        21.0%
        0.70%
        1.0
        97.5
        100.0%
        95.6%
        97.5
        98.5
        MHW320-RG
        24.3%
        0.71%
        1.1
        111.0
        100.0%
        95.1%
        111.0
        112.2
        MHW321-RG
        24.8%
        0.73%
        1.9
        169.4
        100.0%
        94.6%
        169.4
        171.3
        MHW322-RG
        20.4%
        0.73%
        1.2
        99.9
        100.0%
        95.3%
        99.9
        101.1
        MHW323-RG
        21.8%
        0.72%
        1.1
        107.5
        100.0%
        95.1%
        107.5
        108.7
        MHW324-RG
        23.1%
        0.73%
        1.1
        101.7
        100.0%
        94.7%
        101.7
        102.8
        MHW325-RG
        23.4%
        0.72%
        1.0
        98.0
        100.0%
        94.9%
        98.0
        99.0
        MHW326-RG
        26.8%
        0.73%
        0.9
        86.1
        100.0%
        94.7%
        86.1
        87.0
        MHW327-RG
        25.3%
        0.74%
        1.0
        86.8
        100.0%
        94.8%
        86.8
        87.7
        MHW328-RG
        25.6%
        3.16%
        3.9
        88.3
        100.0%
        87.7%
        88.3
        92.2
        MHW329-RG
        25.6%
        0.71%
        1.1
        102.0
        100.0%
        95.1%
        102.0
        103.1
        MHW330-RG
        23.4%
        0.73%
        1.0
        88.8
        100.0%
        94.9%
        88.8
        89.8
        MHW331-RG
        20.1%
        0.73%
        1.0
        85.4
        100.0%
        95.4%
        85.4
        86.4
        MHW332-RG
        27.5%
        0.72%
        0.9
        84.9
        100.0%
        94.5%
        84.9
        85.8
        MHW333-RG
        25.1%
        0.70%
        0.8
        82.1
        100.0%
        95.1%
        82.1
        82.9
        MHW334-RG
        23.4%
        0.72%
        1.0
        91.5
        100.0%
        94.9%
        91.5
        92.5
        MHW335-RG
        14.2%
        3.13%
        4.9
        84.3
        100.0%
        82.8%
        84.3
        89.2
        MHW336-RG
        15.2%
        0.74%
        1.6
        90.7
        100.0%
        91.1%
        90.7
        92.3
        MHW337-RG
        13.4%
        0.74%
        1.1
        76.9
        100.0%
        93.0%
        76.9
        78.1
        MHW338-RG
        13.0%
        0.74%
        1.5
        87.8
        100.0%
        91.4%
        87.8
        89.2
        MHW339-RG
        12.0%
        0.75%
        1.3
        83.7
        100.0%
        93.4%
        83.7
        85.0
        MHW340-RG
        14.5%
        0.72%
        3.6
        90.3
        100.0%
        81.8%
        90.3
        93.9
        MHW341-RG
        12.8%
        0.72%
        1.5
        94.6
        100.0%
        92.3%
        94.6
        96.1
        MHW342-RG
        13.6%
        0.74%
        1.6
        99.6
        100.0%
        92.0%
        99.6
        101.2
        MHW343-RG
        13.1%
        0.73%
        4.9
        97.0
        100.0%
        82.2%
        97.0
        101.9
        MHW344-RG
        13.0%
        0.73%
        2.0
        106.0
        100.0%
        91.7%
        106.0
        108.0
        MHW345-RG
        19.8%
        0.73%
        1.0
        93.8
        100.0%
        95.1%
        93.8
        94.8
        MHW347-RG
        18.4%
        0.71%
        0.9
        82.5
        100.0%
        95.5%
        82.5
        83.4
        MHW348-RG
        21.1%
        0.73%
        0.9
        81.9
        100.0%
        94.9%
        81.9
        82.8
        MHW349-RG
        20.3%
        0.72%
        0.8
        73.5
        100.0%
        95.2%
        73.5
        74.4
        MHW350-RG
        18.1%
        0.71%
        0.9
        78.7
        100.0%
        95.5%
        78.7
        79.6
        MHW351-RG
        22.2%
        0.71%
        0.9
        85.2
        100.0%
        95.2%
        85.2
        86.1
        MHW352-RG
        20.0%
        0.72%
        0.9
        85.3
        100.0%
        95.4%
        85.3
        86.2
        MHW353-RG
        19.3%
        0.72%
        0.8
        75.7
        100.0%
        95.4%
        75.7
        76.5
        MHW407-RG
        19.9%
        0.71%
        0.9
        86.4
        100.0%
        95.2%
        86.4
        87.3
        MHW410-RG
        20.9%
        0.70%
        0.9
        88.1
        100.0%
        95.4%
        88.1
        89.0
        MHW419-RG
        20.7%
        0.72%
        0.9
        85.4
        100.0%
        95.2%
        85.4
        86.4
        MHW420-RG
        19.6%
        0.72%
        0.8
        73.2
        100.0%
        95.4%
        73.2
        74.0
        MHW421-RG
        20.7%
        0.75%
        0.9
        71.2
        100.0%
        95.0%
        71.2
        72.1
        MHW422-RG
        20.8%
        0.73%
        0.9
        79.1
        100.0%
        95.3%
        79.1
        80.0
        MHW424-RG
        19.2%
        0.72%
        0.8
        66.6
        100.0%
        95.3%
        66.6
        67.3
        MHW425-RG
        19.7%
        0.73%
        0.8
        69.1
        100.0%
        95.0%
        69.1
        69.9
        MHW426-RG
        21.4%
        0.72%
        0.8
        70.1
        100.0%
        94.8%
        70.1
        70.9
        MHW427-RG
        19.2%
        0.72%
        0.9
        72.4
        100.0%
        95.1%
        72.4
        73.3
        MHW429-RG
        18.7%
        0.74%
        1.1
        88.4
        100.0%
        95.0%
        88.4
        89.5
        MHW431-RG
        18.3%
        0.74%
        0.9
        76.8
        100.0%
        95.3%
        76.8
        77.7
        MHW432-RG
        19.5%
        0.72%
        1.0
        83.2
        100.0%
        95.1%
        83.2
        84.1

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        loading..

        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

        Percent Mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        loading..

        Alignment metrics

        This module parses the output from samtools stats. All numbers in millions.

        loading..

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

        loading..

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.