Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_all_samples_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        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

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.13

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        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 2023-05-04, 13:38 BST based on data in:

        General Statistics

        Showing 352/352 rows and 4/5 columns.
        Sample Name% Dups% GCRead LengthM Seqs
        AUS_WAL_OA_001_1
        10.6%
        23%
        125 bp
        0.0
        AUS_WAL_OA_001_2
        10.5%
        24%
        125 bp
        0.0
        AUS_WAL_OA_002_1
        11.3%
        24%
        125 bp
        0.0
        AUS_WAL_OA_002_2
        11.1%
        24%
        125 bp
        0.0
        AUS_WAL_OA_003_1
        15.3%
        24%
        125 bp
        0.0
        AUS_WAL_OA_003_2
        15.6%
        24%
        125 bp
        0.0
        AUS_WAL_OA_004_1
        18.8%
        23%
        125 bp
        0.0
        AUS_WAL_OA_004_2
        17.8%
        24%
        125 bp
        0.0
        AUS_WAL_OA_005_1
        11.7%
        23%
        125 bp
        0.0
        AUS_WAL_OA_005_2
        13.1%
        24%
        125 bp
        0.0
        AUS_WAL_OA_006_1
        11.4%
        23%
        125 bp
        0.0
        AUS_WAL_OA_006_2
        11.6%
        24%
        125 bp
        0.0
        AUS_WAL_OA_007_1
        10.9%
        24%
        125 bp
        0.0
        AUS_WAL_OA_007_2
        11.2%
        24%
        125 bp
        0.0
        AUS_WAL_OA_008_1
        7.2%
        24%
        112 bp
        0.0
        AUS_WAL_OA_008_2
        6.9%
        24%
        112 bp
        0.0
        AUS_WAL_OA_009_1
        10.9%
        24%
        125 bp
        0.0
        AUS_WAL_OA_009_2
        10.6%
        24%
        125 bp
        0.0
        AUS_WAL_OA_010_1
        11.0%
        24%
        125 bp
        0.0
        AUS_WAL_OA_010_2
        10.7%
        24%
        125 bp
        0.0
        BEN_BEN_OA_001_1
        49.6%
        22%
        125 bp
        0.0
        BEN_BEN_OA_001_2
        49.1%
        21%
        125 bp
        0.0
        BEN_BEN_OA_004_1
        65.3%
        22%
        125 bp
        0.0
        BEN_BEN_OA_004_2
        63.0%
        22%
        125 bp
        0.0
        BEN_BEN_OA_005_1
        86.9%
        22%
        125 bp
        0.0
        BEN_BEN_OA_005_2
        83.6%
        22%
        125 bp
        0.0
        BEN_BEN_OA_007_1
        13.4%
        22%
        125 bp
        0.0
        BEN_BEN_OA_007_2
        14.5%
        22%
        125 bp
        0.0
        BEN_BEN_OA_008_1
        26.8%
        22%
        125 bp
        0.0
        BEN_BEN_OA_008_2
        26.2%
        22%
        125 bp
        0.0
        BEN_BEN_OA_009_1
        41.7%
        21%
        125 bp
        0.0
        BEN_BEN_OA_009_2
        40.9%
        21%
        125 bp
        0.0
        BEN_BEN_OA_010_1
        21.9%
        22%
        125 bp
        0.0
        BEN_BEN_OA_010_2
        21.2%
        22%
        125 bp
        0.0
        BEN_BEN_OA_011_1
        64.1%
        22%
        125 bp
        0.0
        BEN_BEN_OA_011_2
        62.9%
        22%
        125 bp
        0.0
        BEN_BEN_OA_013_1
        83.7%
        22%
        125 bp
        0.0
        BEN_BEN_OA_013_2
        82.9%
        22%
        125 bp
        0.0
        BRA_BRA_OA_001_1
        83.9%
        22%
        125 bp
        0.0
        BRA_BRA_OA_001_2
        82.5%
        22%
        125 bp
        0.0
        BRA_BRA_OA_004_1
        66.0%
        23%
        125 bp
        0.0
        BRA_BRA_OA_004_2
        65.0%
        23%
        125 bp
        0.0
        BRA_BRA_OA_005_1
        14.5%
        22%
        125 bp
        0.0
        BRA_BRA_OA_005_2
        14.2%
        23%
        125 bp
        0.0
        BRA_BRA_OA_007_1
        17.2%
        22%
        125 bp
        0.0
        BRA_BRA_OA_007_2
        16.3%
        22%
        125 bp
        0.0
        BRA_BRA_OA_008_1
        74.4%
        22%
        125 bp
        0.0
        BRA_BRA_OA_008_2
        71.7%
        22%
        125 bp
        0.0
        BRA_BRA_OA_009_1
        69.7%
        22%
        125 bp
        0.0
        BRA_BRA_OA_009_2
        69.0%
        22%
        125 bp
        0.0
        BRA_BRA_OA_010_1
        77.5%
        28%
        125 bp
        0.0
        BRA_BRA_OA_010_2
        74.7%
        27%
        125 bp
        0.0
        BRA_BRA_OA_011_1
        81.2%
        22%
        125 bp
        0.0
        BRA_BRA_OA_011_2
        79.2%
        22%
        125 bp
        0.0
        BRA_BRA_OA_012_1
        86.6%
        22%
        125 bp
        0.0
        BRA_BRA_OA_012_2
        83.8%
        22%
        125 bp
        0.0
        BRA_BRA_OA_013_1
        84.5%
        21%
        125 bp
        0.0
        BRA_BRA_OA_013_2
        83.6%
        22%
        125 bp
        0.0
        CAP_CAP_CH_002_1
        15.5%
        22%
        125 bp
        0.0
        CAP_CAP_CH_002_2
        14.7%
        22%
        125 bp
        0.0
        CAP_CAP_CH_003_1
        45.7%
        23%
        125 bp
        0.0
        CAP_CAP_CH_003_2
        44.8%
        23%
        125 bp
        0.0
        CAP_CAP_CH_005_1
        29.5%
        22%
        125 bp
        0.0
        CAP_CAP_CH_005_2
        29.9%
        22%
        125 bp
        0.0
        CAP_CAP_CH_006_1
        24.0%
        22%
        125 bp
        0.0
        CAP_CAP_CH_006_2
        23.5%
        23%
        125 bp
        0.0
        CAP_CAP_CH_007_1
        11.0%
        23%
        125 bp
        0.0
        CAP_CAP_CH_007_2
        11.3%
        23%
        125 bp
        0.0
        CAP_CAP_CH_008_1
        47.9%
        23%
        125 bp
        0.0
        CAP_CAP_CH_008_2
        46.5%
        23%
        125 bp
        0.0
        CAP_CAP_CH_009_1
        83.5%
        22%
        125 bp
        0.0
        CAP_CAP_CH_009_2
        81.1%
        22%
        125 bp
        0.0
        CAP_CAP_CH_011_1
        85.5%
        22%
        125 bp
        0.0
        CAP_CAP_CH_011_2
        83.7%
        22%
        125 bp
        0.0
        CAP_CAP_CH_013_1
        48.1%
        22%
        125 bp
        0.0
        CAP_CAP_CH_013_2
        47.3%
        22%
        125 bp
        0.0
        CAP_CAP_CH_014_1
        61.4%
        22%
        125 bp
        0.0
        CAP_CAP_CH_014_2
        59.5%
        22%
        125 bp
        0.0
        FRA_BER_CH_001_1
        17.8%
        22%
        125 bp
        0.0
        FRA_BER_CH_001_2
        16.6%
        22%
        125 bp
        0.0
        FRA_BER_CH_002_1
        11.4%
        23%
        125 bp
        0.0
        FRA_BER_CH_002_2
        10.8%
        23%
        125 bp
        0.0
        FRA_BER_CH_003_1
        11.2%
        22%
        125 bp
        0.0
        FRA_BER_CH_003_2
        11.2%
        22%
        125 bp
        0.0
        FRA_BER_CH_004_1
        14.0%
        23%
        125 bp
        0.0
        FRA_BER_CH_004_2
        13.4%
        23%
        125 bp
        0.0
        FRA_BOL_CH_001_1
        12.9%
        22%
        125 bp
        0.0
        FRA_BOL_CH_001_2
        11.6%
        22%
        125 bp
        0.0
        FRA_BOL_CH_002_1
        10.6%
        22%
        125 bp
        0.0
        FRA_BOL_CH_002_2
        9.9%
        22%
        125 bp
        0.0
        FRA_BOL_CH_003_1
        10.6%
        22%
        125 bp
        0.0
        FRA_BOL_CH_003_2
        10.1%
        22%
        125 bp
        0.0
        FRA_BOL_CH_004_1
        5.9%
        22%
        106 bp
        0.0
        FRA_BOL_CH_004_2
        5.8%
        22%
        106 bp
        0.0
        FRA_CER_CH_001_1
        19.0%
        21%
        125 bp
        0.0
        FRA_CER_CH_001_2
        19.2%
        21%
        125 bp
        0.0
        FRA_CER_CH_002_1
        40.1%
        21%
        125 bp
        0.0
        FRA_CER_CH_002_2
        39.6%
        21%
        125 bp
        0.0
        FRA_CER_CH_003_1
        9.5%
        22%
        125 bp
        0.0
        FRA_CER_CH_003_2
        8.9%
        22%
        125 bp
        0.0
        FRA_CER_CH_004_1
        14.2%
        23%
        125 bp
        0.0
        FRA_CER_CH_004_2
        13.4%
        23%
        125 bp
        0.0
        FRG_AVE_OA_001_1
        10.7%
        22%
        125 bp
        0.0
        FRG_AVE_OA_001_2
        10.3%
        22%
        125 bp
        0.0
        FRG_AVE_OA_002_1
        13.9%
        22%
        125 bp
        0.0
        FRG_AVE_OA_002_2
        14.0%
        22%
        125 bp
        0.0
        FRG_AVE_OA_003_1
        13.3%
        22%
        125 bp
        0.0
        FRG_AVE_OA_003_2
        13.2%
        22%
        125 bp
        0.0
        FRG_AVE_OA_004_1
        11.6%
        22%
        125 bp
        0.0
        FRG_AVE_OA_004_2
        10.6%
        23%
        125 bp
        0.0
        FRG_CES_OA_001_1
        10.1%
        22%
        125 bp
        0.0
        FRG_CES_OA_001_2
        8.9%
        22%
        125 bp
        0.0
        FRG_CES_OA_002_1
        17.3%
        22%
        125 bp
        0.0
        FRG_CES_OA_002_2
        16.9%
        23%
        125 bp
        0.0
        FRG_CES_OA_003_1
        20.5%
        23%
        125 bp
        0.0
        FRG_CES_OA_003_2
        19.8%
        23%
        125 bp
        0.0
        FRG_CES_OA_004_1
        13.2%
        22%
        125 bp
        0.0
        FRG_CES_OA_004_2
        11.8%
        22%
        125 bp
        0.0
        FRG_DAV_OA_001_1
        12.2%
        23%
        125 bp
        0.0
        FRG_DAV_OA_001_2
        11.5%
        23%
        125 bp
        0.0
        FRG_DAV_OA_002_1
        45.4%
        23%
        125 bp
        0.0
        FRG_DAV_OA_002_2
        43.8%
        23%
        125 bp
        0.0
        FRG_DAV_OA_003_1
        10.9%
        22%
        125 bp
        0.0
        FRG_DAV_OA_003_2
        10.7%
        23%
        125 bp
        0.0
        FRG_DAV_OA_004_1
        8.4%
        22%
        103 bp
        0.0
        FRG_DAV_OA_004_2
        8.2%
        22%
        103 bp
        0.0
        FRG_DEJ_OA_001_1
        7.9%
        22%
        109 bp
        0.0
        FRG_DEJ_OA_001_2
        7.4%
        22%
        109 bp
        0.0
        FRG_DEJ_OA_002_1
        6.5%
        22%
        110 bp
        0.0
        FRG_DEJ_OA_002_2
        6.1%
        22%
        110 bp
        0.0
        FRG_DEJ_OA_003_1
        6.0%
        22%
        101 bp
        0.0
        FRG_DEJ_OA_003_2
        5.6%
        22%
        101 bp
        0.0
        FRG_DEJ_OA_004_1
        11.5%
        23%
        125 bp
        0.0
        FRG_DEJ_OA_004_2
        11.1%
        23%
        125 bp
        0.0
        FRG_MEY_OA_001_1
        18.8%
        23%
        125 bp
        0.0
        FRG_MEY_OA_001_2
        18.6%
        23%
        125 bp
        0.0
        FRG_MEY_OA_002_1
        14.9%
        23%
        125 bp
        0.0
        FRG_MEY_OA_002_2
        13.4%
        23%
        125 bp
        0.0
        FRG_MEY_OA_003_1
        6.8%
        22%
        105 bp
        0.0
        FRG_MEY_OA_003_2
        5.9%
        22%
        105 bp
        0.0
        FRG_ROB_OA_001_1
        11.2%
        22%
        125 bp
        0.0
        FRG_ROB_OA_001_2
        10.4%
        22%
        125 bp
        0.0
        FRG_ROB_OA_002_1
        10.1%
        23%
        125 bp
        0.0
        FRG_ROB_OA_002_2
        9.7%
        23%
        125 bp
        0.0
        FRG_ROB_OA_003_1
        11.2%
        23%
        125 bp
        0.0
        FRG_ROB_OA_003_2
        9.9%
        23%
        125 bp
        0.0
        FRG_ROB_OA_004_1
        11.2%
        23%
        125 bp
        0.0
        FRG_ROB_OA_004_2
        10.6%
        23%
        125 bp
        0.0
        GB_ISEN1_001_1
        8.6%
        21%
        151 bp
        0.0
        GB_ISEN1_001_2
        7.2%
        22%
        151 bp
        0.0
        GB_ISEN1_002_1
        9.4%
        21%
        151 bp
        0.0
        GB_ISEN1_002_2
        7.3%
        22%
        151 bp
        0.0
        GB_ISEN1_003_1
        8.3%
        22%
        151 bp
        0.0
        GB_ISEN1_003_2
        8.1%
        22%
        151 bp
        0.0
        GB_ISEN1_004_1
        9.1%
        22%
        151 bp
        0.0
        GB_ISEN1_004_2
        7.7%
        22%
        151 bp
        0.0
        GB_ISEN1_005_1
        9.0%
        22%
        151 bp
        0.0
        GB_ISEN1_005_2
        7.9%
        22%
        151 bp
        0.0
        GB_ISEN1_006_1
        8.7%
        22%
        151 bp
        0.0
        GB_ISEN1_006_2
        7.5%
        22%
        151 bp
        0.0
        GB_ISEN1_007_1
        9.2%
        21%
        151 bp
        0.0
        GB_ISEN1_007_2
        7.2%
        22%
        151 bp
        0.0
        GB_ISEN1_008_1
        10.0%
        21%
        151 bp
        0.0
        GB_ISEN1_008_2
        8.6%
        22%
        151 bp
        0.0
        GB_ISEN1_009_1
        8.1%
        21%
        151 bp
        0.0
        GB_ISEN1_009_2
        7.5%
        22%
        151 bp
        0.0
        GB_ISEN1_010_1
        9.4%
        22%
        151 bp
        0.0
        GB_ISEN1_010_2
        7.7%
        22%
        151 bp
        0.0
        GB_ISEN1_011_1
        8.5%
        21%
        151 bp
        0.0
        GB_ISEN1_011_2
        7.9%
        22%
        151 bp
        0.0
        IND_IND_CH_001_1
        52.2%
        24%
        125 bp
        0.0
        IND_IND_CH_001_2
        50.2%
        23%
        125 bp
        0.0
        IND_IND_CH_002_1
        5.7%
        22%
        99 bp
        0.0
        IND_IND_CH_002_2
        5.6%
        22%
        99 bp
        0.0
        IND_IND_CH_003_1
        29.7%
        23%
        125 bp
        0.0
        IND_IND_CH_003_2
        28.2%
        23%
        125 bp
        0.0
        IND_IND_CH_004_1
        24.4%
        23%
        125 bp
        0.0
        IND_IND_CH_004_2
        22.5%
        24%
        125 bp
        0.0
        IND_IND_CH_005_1
        8.3%
        23%
        104 bp
        0.0
        IND_IND_CH_005_2
        7.4%
        23%
        104 bp
        0.0
        IND_IND_CH_006_1
        25.7%
        22%
        125 bp
        0.0
        IND_IND_CH_006_2
        24.1%
        22%
        125 bp
        0.0
        IND_IND_CH_007_1
        11.8%
        22%
        125 bp
        0.0
        IND_IND_CH_007_2
        11.4%
        22%
        125 bp
        0.0
        MOR_MAR_OA_001_1
        12.2%
        23%
        125 bp
        0.0
        MOR_MAR_OA_001_2
        12.4%
        23%
        125 bp
        0.0
        MOR_MAR_OA_002_1
        44.8%
        22%
        125 bp
        0.0
        MOR_MAR_OA_002_2
        43.0%
        22%
        125 bp
        0.0
        MOR_MAR_OA_003_1
        14.7%
        22%
        125 bp
        0.0
        MOR_MAR_OA_003_2
        13.9%
        22%
        125 bp
        0.0
        MOR_MAR_OA_005_1
        19.3%
        22%
        125 bp
        0.0
        MOR_MAR_OA_005_2
        18.1%
        22%
        125 bp
        0.0
        MOR_MAR_OA_006_1
        39.8%
        23%
        125 bp
        0.0
        MOR_MAR_OA_006_2
        37.4%
        23%
        125 bp
        0.0
        MOR_MAR_OA_008_1
        10.9%
        22%
        125 bp
        0.0
        MOR_MAR_OA_008_2
        10.4%
        22%
        125 bp
        0.0
        MOR_MAR_OA_009_1
        8.3%
        22%
        99 bp
        0.0
        MOR_MAR_OA_009_2
        7.1%
        23%
        99 bp
        0.0
        MOR_MAR_OA_010_1
        15.8%
        22%
        125 bp
        0.0
        MOR_MAR_OA_010_2
        14.9%
        22%
        125 bp
        0.0
        MOR_MAR_OA_011_1
        18.0%
        21%
        125 bp
        0.0
        MOR_MAR_OA_011_2
        16.7%
        22%
        125 bp
        0.0
        MOR_MAR_OA_012_1
        11.2%
        22%
        125 bp
        0.0
        MOR_MAR_OA_012_2
        9.8%
        22%
        125 bp
        0.0
        NAM_NAM_CH_001_1
        7.8%
        22%
        108 bp
        0.0
        NAM_NAM_CH_001_2
        7.6%
        22%
        108 bp
        0.0
        NAM_NAM_CH_002_1
        9.9%
        22%
        125 bp
        0.0
        NAM_NAM_CH_002_2
        9.7%
        22%
        125 bp
        0.0
        NAM_NAM_CH_003_1
        11.0%
        22%
        125 bp
        0.0
        NAM_NAM_CH_003_2
        10.1%
        22%
        125 bp
        0.0
        NAM_NAM_CH_004_1
        11.3%
        23%
        125 bp
        0.0
        NAM_NAM_CH_004_2
        9.8%
        23%
        125 bp
        0.0
        NAM_NAM_CH_005_1
        10.6%
        22%
        125 bp
        0.0
        NAM_NAM_CH_005_2
        10.0%
        22%
        125 bp
        0.0
        NAM_NAM_CH_006_1
        9.2%
        22%
        125 bp
        0.0
        NAM_NAM_CH_006_2
        9.2%
        22%
        125 bp
        0.0
        NAM_NAM_CH_007_1
        10.6%
        22%
        125 bp
        0.0
        NAM_NAM_CH_007_2
        10.2%
        22%
        125 bp
        0.0
        NAM_NAM_CH_008_1
        55.2%
        23%
        125 bp
        0.0
        NAM_NAM_CH_008_2
        54.0%
        24%
        125 bp
        0.0
        NAM_NAM_CH_009_1
        11.4%
        23%
        108 bp
        0.0
        NAM_NAM_CH_009_2
        11.4%
        23%
        108 bp
        0.0
        NAM_NAM_CH_010_1
        8.5%
        22%
        111 bp
        0.0
        NAM_NAM_CH_010_2
        8.2%
        23%
        111 bp
        0.0
        PK_PAK_001_1
        7.6%
        22%
        100 bp
        0.0
        PK_PAK_001_2
        6.3%
        22%
        100 bp
        0.0
        PK_PAK_002_1
        7.9%
        22%
        100 bp
        0.0
        PK_PAK_002_2
        5.8%
        22%
        100 bp
        0.0
        PK_PAK_003_1
        1.3%
        23%
        100 bp
        0.0
        PK_PAK_003_2
        0.9%
        23%
        100 bp
        0.0
        PK_PAK_004_1
        6.9%
        23%
        100 bp
        0.0
        PK_PAK_004_2
        5.7%
        23%
        100 bp
        0.0
        PK_PAK_005_1
        7.3%
        23%
        100 bp
        0.0
        PK_PAK_005_2
        5.5%
        23%
        100 bp
        0.0
        PK_PAK_006_1
        7.3%
        22%
        100 bp
        0.0
        PK_PAK_006_2
        6.3%
        22%
        100 bp
        0.0
        PK_PAK_007_1
        7.1%
        22%
        100 bp
        0.0
        PK_PAK_007_2
        6.1%
        22%
        100 bp
        0.0
        PK_PAK_008_1
        6.8%
        22%
        100 bp
        0.0
        PK_PAK_008_2
        5.8%
        22%
        100 bp
        0.0
        PK_PAK_009_1
        7.3%
        22%
        100 bp
        0.0
        PK_PAK_009_2
        6.4%
        23%
        100 bp
        0.0
        PK_PAK_010_1
        7.7%
        23%
        100 bp
        0.0
        PK_PAK_010_2
        6.1%
        23%
        100 bp
        0.0
        POR_ACO_CH_001_1
        12.2%
        22%
        125 bp
        0.0
        POR_ACO_CH_001_2
        12.9%
        22%
        125 bp
        0.0
        POR_ACO_CH_002_1
        34.9%
        22%
        125 bp
        0.0
        POR_ACO_CH_002_2
        33.5%
        22%
        125 bp
        0.0
        POR_ACO_CH_003_1
        31.4%
        22%
        125 bp
        0.0
        POR_ACO_CH_003_2
        31.7%
        22%
        125 bp
        0.0
        POR_ACO_CH_004_1
        53.6%
        22%
        125 bp
        0.0
        POR_ACO_CH_004_2
        53.2%
        22%
        125 bp
        0.0
        POR_ACO_CH_005_1
        9.8%
        22%
        111 bp
        0.0
        POR_ACO_CH_005_2
        9.9%
        22%
        111 bp
        0.0
        STA_KOK_OA_001_1
        10.6%
        22%
        125 bp
        0.0
        STA_KOK_OA_001_2
        10.6%
        22%
        125 bp
        0.0
        STA_KOK_OA_002_1
        13.4%
        23%
        125 bp
        0.0
        STA_KOK_OA_002_2
        13.0%
        23%
        125 bp
        0.0
        STA_KOK_OA_004_1
        14.4%
        23%
        125 bp
        0.0
        STA_KOK_OA_004_2
        12.3%
        23%
        125 bp
        0.0
        STA_KOK_OA_005_1
        11.2%
        22%
        125 bp
        0.0
        STA_KOK_OA_005_2
        11.1%
        22%
        125 bp
        0.0
        STA_KOK_OA_006_1
        11.8%
        23%
        125 bp
        0.0
        STA_KOK_OA_006_2
        11.1%
        23%
        125 bp
        0.0
        STA_KOK_OA_007_1
        11.4%
        22%
        125 bp
        0.0
        STA_KOK_OA_007_2
        9.8%
        23%
        125 bp
        0.0
        STA_KOK_OA_008_1
        11.2%
        22%
        88 bp
        0.0
        STA_KOK_OA_008_2
        10.5%
        23%
        88 bp
        0.0
        STA_KOK_OA_009_1
        10.9%
        23%
        125 bp
        0.0
        STA_KOK_OA_009_2
        10.4%
        23%
        125 bp
        0.0
        STA_KOK_OA_010_1
        11.5%
        22%
        125 bp
        0.0
        STA_KOK_OA_010_2
        10.6%
        22%
        125 bp
        0.0
        STA_KOK_OA_011_1
        8.7%
        23%
        108 bp
        0.0
        STA_KOK_OA_011_2
        8.6%
        23%
        108 bp
        0.0
        STA_OND_OA_001_1
        20.3%
        23%
        125 bp
        0.0
        STA_OND_OA_001_2
        20.8%
        24%
        125 bp
        0.0
        STA_OND_OA_002_1
        46.4%
        23%
        125 bp
        0.0
        STA_OND_OA_002_2
        44.8%
        24%
        125 bp
        0.0
        STA_OND_OA_003_1
        15.7%
        23%
        125 bp
        0.0
        STA_OND_OA_003_2
        15.6%
        24%
        125 bp
        0.0
        STA_OND_OA_004_1
        13.5%
        23%
        125 bp
        0.0
        STA_OND_OA_004_2
        13.4%
        24%
        125 bp
        0.0
        STA_OND_OA_005_1
        10.3%
        24%
        125 bp
        0.0
        STA_OND_OA_005_2
        10.9%
        24%
        125 bp
        0.0
        STA_OND_OA_006_1
        13.3%
        24%
        125 bp
        0.0
        STA_OND_OA_006_2
        12.7%
        24%
        125 bp
        0.0
        STA_OND_OA_007_1
        27.1%
        24%
        125 bp
        0.0
        STA_OND_OA_007_2
        27.2%
        25%
        125 bp
        0.0
        STA_OND_OA_008_1
        19.2%
        24%
        125 bp
        0.0
        STA_OND_OA_008_2
        18.2%
        24%
        125 bp
        0.0
        STA_OND_OA_010_1
        11.8%
        23%
        125 bp
        0.0
        STA_OND_OA_010_2
        10.5%
        24%
        125 bp
        0.0
        STA_OND_OA_011_1
        13.2%
        23%
        125 bp
        0.0
        STA_OND_OA_011_2
        12.8%
        24%
        125 bp
        0.0
        STA_WHR_OA_001_1
        13.5%
        24%
        125 bp
        0.0
        STA_WHR_OA_001_2
        13.1%
        24%
        125 bp
        0.0
        STA_WHR_OA_002_1
        13.5%
        24%
        125 bp
        0.0
        STA_WHR_OA_002_2
        13.6%
        25%
        125 bp
        0.0
        STA_WHR_OA_003_1
        14.1%
        23%
        125 bp
        0.0
        STA_WHR_OA_003_2
        14.3%
        24%
        125 bp
        0.0
        STA_WHR_OA_004_1
        13.5%
        23%
        125 bp
        0.0
        STA_WHR_OA_004_2
        12.2%
        23%
        125 bp
        0.0
        STA_WHR_OA_005_1
        11.1%
        23%
        125 bp
        0.0
        STA_WHR_OA_005_2
        11.7%
        24%
        125 bp
        0.0
        STA_WHR_OA_006_1
        13.3%
        23%
        125 bp
        0.0
        STA_WHR_OA_006_2
        12.9%
        23%
        125 bp
        0.0
        STA_WHR_OA_007_1
        19.7%
        23%
        125 bp
        0.0
        STA_WHR_OA_007_2
        17.5%
        24%
        125 bp
        0.0
        STA_WHR_OA_008_1
        22.5%
        23%
        125 bp
        0.0
        STA_WHR_OA_008_2
        23.0%
        23%
        125 bp
        0.0
        STA_WHR_OA_009_1
        38.3%
        23%
        125 bp
        0.0
        STA_WHR_OA_009_2
        37.5%
        24%
        125 bp
        0.0
        STA_WHR_OA_010_1
        66.8%
        24%
        125 bp
        0.0
        STA_WHR_OA_010_2
        65.7%
        25%
        125 bp
        0.0
        STO_STO_CH_001_1
        11.8%
        23%
        125 bp
        0.0
        STO_STO_CH_001_2
        11.8%
        23%
        125 bp
        0.0
        STO_STO_CH_002_1
        19.5%
        23%
        125 bp
        0.0
        STO_STO_CH_002_2
        18.8%
        23%
        125 bp
        0.0
        STO_STO_CH_003_1
        13.5%
        24%
        125 bp
        0.0
        STO_STO_CH_003_2
        12.9%
        24%
        125 bp
        0.0
        STO_STO_CH_004_1
        12.1%
        23%
        125 bp
        0.0
        STO_STO_CH_004_2
        11.6%
        24%
        125 bp
        0.0
        STO_STO_CH_005_1
        14.3%
        24%
        125 bp
        0.0
        STO_STO_CH_005_2
        13.6%
        24%
        125 bp
        0.0
        STO_STO_CH_006_1
        11.7%
        23%
        125 bp
        0.0
        STO_STO_CH_006_2
        12.1%
        23%
        125 bp
        0.0
        STO_STO_CH_007_1
        7.9%
        24%
        112 bp
        0.0
        STO_STO_CH_007_2
        8.1%
        24%
        112 bp
        0.0
        STO_STO_CH_008_1
        6.2%
        23%
        97 bp
        0.0
        STO_STO_CH_008_2
        5.1%
        24%
        97 bp
        0.0
        STO_STO_CH_009_1
        13.2%
        23%
        125 bp
        0.0
        STO_STO_CH_009_2
        12.3%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_001_1
        13.0%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_001_2
        11.1%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_002_1
        14.9%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_002_2
        13.8%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_003_1
        15.2%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_003_2
        16.4%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_004_1
        19.1%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_004_2
        17.7%
        25%
        125 bp
        0.0
        ZAI_ZAI_OA_005_1
        12.5%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_005_2
        11.9%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_006_1
        14.1%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_006_2
        12.7%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_007_1
        10.9%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_007_2
        10.7%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_008_1
        12.9%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_008_2
        12.4%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_009_1
        13.7%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_009_2
        13.2%
        24%
        125 bp
        0.0
        ZAI_ZAI_OA_010_1
        25.7%
        23%
        125 bp
        0.0
        ZAI_ZAI_OA_010_2
        25.2%
        24%
        125 bp
        0.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        loading..

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        loading..

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        loading..

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        loading..

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.13 - Written by Phil Ewels, available on GitHub.

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