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        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

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        About MultiQC

        This report was generated using MultiQC, version 1.9

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        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 2021-02-03, 22:14 based on data in: /net/shendure/vol9/seq/NEXTSEQ_FastQ_Output/210127_NS500488_1112_AHG2C7BGXH_wei_demultiplexed


        General Statistics

        Showing 385/385 rows and 8/12 columns.
        Sample Name% Dups% GCM SeqsM ClustersMb Yield ≥ Q30% R1 Yield ≥ Q30% R2 Yield ≥ Q30% Perfect Index
        A01_P3
        0.9
        91.4
        93.8%
        67.3%
        92.8%
        A01_P3_S1_R2_001
        47.9%
        47%
        0.9
        A01_P4
        6.7
        694.6
        94.0%
        72.2%
        93.1%
        A01_P4_S97_R2_001
        65.2%
        47%
        6.7
        A02_P3
        1.2
        110.5
        93.4%
        61.3%
        91.5%
        A02_P3_S2_R2_001
        37.7%
        48%
        1.2
        A02_P4
        2.5
        251.0
        93.5%
        67.7%
        91.1%
        A02_P4_S98_R2_001
        54.3%
        48%
        2.5
        A03_P3
        1.0
        94.8
        93.4%
        64.7%
        87.7%
        A03_P3_S3_R2_001
        43.7%
        48%
        1.0
        A03_P4
        3.7
        385.0
        93.8%
        72.1%
        87.6%
        A03_P4_S99_R2_001
        63.2%
        48%
        3.7
        A04_P3
        0.8
        78.0
        93.2%
        63.5%
        92.9%
        A04_P3_S4_R2_001
        38.7%
        47%
        0.8
        A04_P4
        3.1
        331.4
        94.1%
        73.4%
        93.3%
        A04_P4_S100_R2_001
        64.8%
        48%
        3.1
        A05_P3
        1.4
        132.2
        93.4%
        60.9%
        93.0%
        A05_P3_S5_R2_001
        33.1%
        48%
        1.4
        A05_P4
        2.3
        248.8
        94.5%
        74.9%
        93.3%
        A05_P4_S101_R2_001
        66.5%
        49%
        2.3
        A06_P3
        1.0
        98.2
        93.9%
        66.4%
        92.8%
        A06_P3_S6_R2_001
        48.7%
        48%
        1.0
        A06_P4
        2.4
        251.3
        94.2%
        72.6%
        92.8%
        A06_P4_S102_R2_001
        62.7%
        48%
        2.4
        A07_P3
        0.9
        88.2
        93.8%
        66.7%
        93.0%
        A07_P3_S7_R2_001
        48.4%
        47%
        0.9
        A07_P4
        3.9
        407.7
        94.3%
        73.3%
        93.1%
        A07_P4_S103_R2_001
        66.2%
        47%
        3.9
        A08_P3
        0.9
        92.5
        94.0%
        68.7%
        93.0%
        A08_P3_S8_R2_001
        54.0%
        47%
        0.9
        A08_P4
        5.0
        520.8
        94.3%
        72.8%
        92.8%
        A08_P4_S104_R2_001
        65.4%
        46%
        5.0
        A09_P3
        0.9
        83.6
        93.2%
        63.0%
        92.3%
        A09_P3_S9_R2_001
        38.3%
        48%
        0.9
        A09_P4
        2.4
        256.1
        94.0%
        72.8%
        92.5%
        A09_P4_S105_R2_001
        62.4%
        48%
        2.4
        A10_P3
        0.6
        57.6
        93.4%
        64.0%
        92.7%
        A10_P3_S10_R2_001
        41.8%
        47%
        0.6
        A10_P4
        2.0
        204.5
        94.1%
        70.7%
        92.6%
        A10_P4_S106_R2_001
        58.7%
        48%
        2.0
        A11_P3
        0.7
        64.4
        93.1%
        62.5%
        92.0%
        A11_P3_S11_R2_001
        37.5%
        47%
        0.7
        A11_P4
        2.1
        215.8
        93.6%
        70.3%
        91.9%
        A11_P4_S107_R2_001
        58.6%
        48%
        2.1
        A12_P3
        0.8
        71.6
        93.1%
        62.3%
        92.6%
        A12_P3_S12_R2_001
        36.3%
        47%
        0.8
        A12_P4
        2.7
        288.5
        94.0%
        73.1%
        93.2%
        A12_P4_S108_R2_001
        65.0%
        47%
        2.7
        B01_P3
        2.1
        217.3
        94.1%
        69.8%
        92.7%
        B01_P3_S13_R2_001
        56.1%
        49%
        2.1
        B01_P4
        8.6
        887.3
        94.0%
        71.6%
        93.6%
        B01_P4_S109_R2_001
        66.3%
        48%
        8.6
        B02_P3
        1.5
        148.2
        93.9%
        65.7%
        91.1%
        B02_P3_S14_R2_001
        48.6%
        49%
        1.5
        B02_P4
        3.9
        393.5
        93.8%
        68.4%
        92.5%
        B02_P4_S110_R2_001
        59.2%
        48%
        3.9
        B03_P3
        0.7
        66.3
        93.2%
        64.5%
        87.0%
        B03_P3_S15_R2_001
        42.1%
        49%
        0.7
        B03_P4
        4.8
        503.7
        94.0%
        72.0%
        88.6%
        B03_P4_S111_R2_001
        64.7%
        49%
        4.8
        B04_P3
        0.8
        75.9
        93.3%
        64.5%
        92.5%
        B04_P3_S16_R2_001
        41.7%
        48%
        0.8
        B04_P4
        2.6
        267.2
        94.0%
        71.6%
        93.8%
        B04_P4_S112_R2_001
        61.8%
        48%
        2.6
        B05_P3
        0.9
        90.0
        93.6%
        64.0%
        92.3%
        B05_P3_S17_R2_001
        40.8%
        49%
        0.9
        B05_P4
        2.5
        259.9
        94.1%
        71.5%
        93.4%
        B05_P4_S113_R2_001
        62.4%
        49%
        2.5
        B06_P3
        1.0
        98.0
        93.7%
        63.7%
        92.0%
        B06_P3_S18_R2_001
        40.8%
        49%
        1.0
        B06_P4
        3.6
        379.4
        94.4%
        72.8%
        93.5%
        B06_P4_S114_R2_001
        66.5%
        49%
        3.6
        B07_P3
        0.5
        49.9
        93.8%
        66.0%
        92.2%
        B07_P3_S19_R2_001
        44.4%
        49%
        0.5
        B07_P4
        4.4
        456.8
        94.2%
        72.1%
        93.6%
        B07_P4_S115_R2_001
        66.4%
        47%
        4.4
        B08_P3
        0.7
        63.8
        93.5%
        64.3%
        92.1%
        B08_P3_S20_R2_001
        41.3%
        49%
        0.7
        B08_P4
        4.5
        463.0
        94.1%
        71.5%
        93.4%
        B08_P4_S116_R2_001
        65.2%
        48%
        4.5
        B09_P3
        0.4
        38.5
        93.3%
        64.0%
        91.5%
        B09_P3_S21_R2_001
        38.7%
        50%
        0.4
        B09_P4
        2.8
        285.7
        93.7%
        71.2%
        93.0%
        B09_P4_S117_R2_001
        62.2%
        49%
        2.8
        B10_P3
        1.0
        89.8
        92.9%
        59.6%
        91.4%
        B10_P3_S22_R2_001
        32.0%
        49%
        1.0
        B10_P4
        2.1
        218.9
        94.5%
        73.4%
        93.9%
        B10_P4_S118_R2_001
        65.7%
        50%
        2.1
        B11_P3
        0.8
        75.9
        93.5%
        63.8%
        91.7%
        B11_P3_S23_R2_001
        39.0%
        49%
        0.8
        B11_P4
        0.0
        0.2
        90.1%
        65.0%
        76.6%
        B11_P4_S119_R2_001
        10.5%
        46%
        0.0
        B12_P3
        0.5
        51.9
        93.7%
        66.7%
        92.4%
        B12_P3_S24_R2_001
        46.4%
        49%
        0.5
        B12_P4
        3.1
        327.9
        94.4%
        73.2%
        93.9%
        B12_P4_S120_R2_001
        66.8%
        48%
        3.1
        C01_P3
        1.1
        107.2
        93.7%
        65.7%
        92.9%
        C01_P3_S25_R2_001
        45.7%
        48%
        1.1
        C01_P4
        7.9
        828.9
        94.2%
        72.8%
        93.8%
        C01_P4_S121_R2_001
        68.1%
        47%
        7.9
        C02_P3
        1.6
        153.3
        93.9%
        65.2%
        92.1%
        C02_P3_S26_R2_001
        47.2%
        49%
        1.6
        C02_P4
        4.0
        411.6
        94.3%
        72.0%
        92.7%
        C02_P4_S122_R2_001
        65.4%
        49%
        4.0
        C03_P3
        1.1
        107.9
        93.3%
        63.9%
        88.2%
        C03_P3_S27_R2_001
        41.3%
        48%
        1.1
        C03_P4
        3.5
        367.0
        94.1%
        72.0%
        88.3%
        C03_P4_S123_R2_001
        62.9%
        49%
        3.5
        C04_P3
        1.0
        93.5
        93.6%
        66.5%
        93.2%
        C04_P3_S28_R2_001
        46.8%
        47%
        1.0
        C04_P4
        1.3
        134.8
        93.5%
        68.9%
        93.5%
        C04_P4_S124_R2_001
        54.7%
        48%
        1.3
        C05_P3
        1.2
        116.3
        93.9%
        66.6%
        93.2%
        C05_P3_S29_R2_001
        48.3%
        48%
        1.2
        C05_P4
        2.3
        240.9
        94.5%
        73.2%
        93.8%
        C05_P4_S125_R2_001
        65.3%
        49%
        2.3
        C06_P3
        1.4
        134.4
        93.8%
        65.3%
        92.9%
        C06_P3_S30_R2_001
        45.0%
        48%
        1.4
        C06_P4
        2.7
        277.1
        93.9%
        71.0%
        93.2%
        C06_P4_S126_R2_001
        61.7%
        48%
        2.7
        C07_P3
        0.7
        71.2
        93.8%
        66.1%
        93.1%
        C07_P3_S31_R2_001
        45.2%
        48%
        0.7
        C07_P4
        4.3
        437.2
        93.8%
        70.2%
        93.4%
        C07_P4_S127_R2_001
        62.3%
        47%
        4.3
        C08_P3
        1.0
        98.6
        93.9%
        66.8%
        92.9%
        C08_P3_S32_R2_001
        48.6%
        48%
        1.0
        C08_P4
        2.9
        289.8
        93.6%
        68.7%
        93.2%
        C08_P4_S128_R2_001
        57.3%
        47%
        2.9
        C09_P3
        0.6
        57.8
        93.3%
        63.9%
        92.4%
        C09_P3_S33_R2_001
        39.9%
        48%
        0.6
        C09_P4
        2.1
        222.1
        94.0%
        72.0%
        93.2%
        C09_P4_S129_R2_001
        62.1%
        49%
        2.1
        C10_P3
        0.8
        67.2
        93.0%
        51.5%
        92.9%
        C10_P3_S34_R2_001
        7.9%
        52%
        0.8
        C10_P4
        1.4
        148.2
        94.3%
        71.1%
        93.5%
        C10_P4_S130_R2_001
        58.7%
        48%
        1.4
        C11_P3
        1.1
        101.7
        93.4%
        62.7%
        92.4%
        C11_P3_S35_R2_001
        36.9%
        48%
        1.1
        C11_P4
        4.3
        452.4
        94.3%
        73.1%
        93.3%
        C11_P4_S131_R2_001
        65.1%
        48%
        4.3
        C12_P3
        1.1
        105.6
        92.9%
        61.2%
        92.8%
        C12_P3_S36_R2_001
        34.3%
        47%
        1.1
        C12_P4
        3.0
        314.2
        94.3%
        72.5%
        93.8%
        C12_P4_S132_R2_001
        64.3%
        48%
        3.0
        D01_P3
        1.2
        119.9
        93.6%
        66.5%
        93.4%
        D01_P3_S37_R2_001
        45.3%
        50%
        1.2
        D01_P4
        5.7
        589.2
        93.7%
        70.8%
        92.6%
        D01_P4_S133_R2_001
        63.7%
        48%
        5.7
        D02_P3
        1.2
        111.9
        93.4%
        62.8%
        91.8%
        D02_P3_S38_R2_001
        38.5%
        51%
        1.2
        D02_P4
        3.6
        354.1
        93.7%
        66.9%
        90.2%
        D02_P4_S134_R2_001
        54.3%
        51%
        3.6
        D03_P3
        0.3
        31.7
        93.4%
        66.0%
        87.8%
        D03_P3_S39_R2_001
        44.2%
        51%
        0.3
        D03_P4
        4.8
        497.3
        93.9%
        71.4%
        86.9%
        D03_P4_S135_R2_001
        63.4%
        49%
        4.8
        D04_P3
        0.4
        37.5
        93.7%
        67.1%
        93.6%
        D04_P3_S40_R2_001
        46.2%
        50%
        0.4
        D04_P4
        2.7
        283.6
        94.0%
        71.8%
        92.7%
        D04_P4_S136_R2_001
        61.9%
        49%
        2.7
        D05_P3
        0.5
        44.5
        93.3%
        63.7%
        93.3%
        D05_P3_S41_R2_001
        37.5%
        51%
        0.5
        D05_P4
        2.1
        217.8
        94.3%
        73.1%
        92.8%
        D05_P4_S137_R2_001
        64.6%
        50%
        2.1
        D06_P3
        0.4
        43.3
        93.9%
        67.8%
        93.2%
        D06_P3_S42_R2_001
        49.5%
        51%
        0.4
        D06_P4
        2.7
        289.4
        94.5%
        73.4%
        92.6%
        D06_P4_S138_R2_001
        65.9%
        50%
        2.7
        D07_P3
        1.8
        173.2
        93.2%
        64.5%
        92.7%
        D07_P3_S43_R2_001
        39.2%
        50%
        1.8
        D07_P4
        4.0
        406.5
        93.7%
        69.7%
        92.2%
        D07_P4_S139_R2_001
        61.4%
        48%
        4.0
        D08_P3
        0.7
        70.9
        93.5%
        66.0%
        93.1%
        D08_P3_S44_R2_001
        43.3%
        50%
        0.7
        D08_P4
        4.1
        422.3
        94.1%
        71.6%
        92.4%
        D08_P4_S140_R2_001
        64.3%
        49%
        4.1
        D09_P3
        0.5
        43.4
        93.0%
        62.9%
        92.6%
        D09_P3_S45_R2_001
        33.1%
        51%
        0.5
        D09_P4
        0.6
        58.1
        93.9%
        72.5%
        91.6%
        D09_P4_S141_R2_001
        60.6%
        51%
        0.6
        D10_P3
        1.0
        97.2
        93.6%
        65.1%
        92.7%
        D10_P3_S46_R2_001
        42.8%
        51%
        1.0
        D10_P4
        1.3
        130.8
        94.0%
        69.9%
        92.0%
        D10_P4_S142_R2_001
        55.9%
        49%
        1.3
        D11_P3
        0.9
        84.7
        93.2%
        63.2%
        92.5%
        D11_P3_S47_R2_001
        35.4%
        50%
        0.9
        D11_P4
        1.8
        180.7
        93.9%
        70.3%
        91.8%
        D11_P4_S143_R2_001
        56.3%
        50%
        1.8
        D12_P3
        0.7
        70.1
        93.3%
        65.2%
        93.3%
        D12_P3_S48_R2_001
        41.3%
        50%
        0.7
        D12_P4
        2.2
        228.0
        93.8%
        70.1%
        92.4%
        D12_P4_S144_R2_001
        58.6%
        49%
        2.2
        E01_P3
        1.0
        101.8
        93.6%
        66.2%
        93.3%
        E01_P3_S49_R2_001
        46.5%
        48%
        1.0
        E01_P4
        6.8
        710.9
        94.2%
        73.0%
        93.5%
        E01_P4_S145_R2_001
        68.4%
        48%
        6.8
        E02_P3
        1.6
        154.8
        93.9%
        65.3%
        92.0%
        E02_P3_S50_R2_001
        47.5%
        50%
        1.6
        E02_P4
        3.1
        328.2
        94.4%
        73.1%
        92.5%
        E02_P4_S146_R2_001
        67.6%
        51%
        3.1
        E03_P3
        0.6
        60.7
        92.3%
        62.3%
        87.6%
        E03_P3_S51_R2_001
        37.3%
        49%
        0.6
        E03_P4
        3.2
        331.5
        93.8%
        72.7%
        87.7%
        E03_P4_S147_R2_001
        65.6%
        50%
        3.2
        E04_P3
        0.4
        39.7
        93.6%
        66.2%
        93.5%
        E04_P3_S52_R2_001
        45.2%
        49%
        0.4
        E04_P4
        3.0
        312.2
        94.1%
        73.1%
        93.6%
        E04_P4_S148_R2_001
        64.8%
        49%
        3.0
        E05_P3
        0.8
        74.2
        93.4%
        63.2%
        93.4%
        E05_P3_S53_R2_001
        39.4%
        49%
        0.8
        E05_P4
        0.6
        50.8
        92.7%
        59.2%
        92.3%
        E05_P4_S149_R2_001
        27.6%
        52%
        0.6
        E06_P3
        0.8
        77.4
        93.6%
        63.6%
        93.0%
        E06_P3_S54_R2_001
        40.3%
        50%
        0.8
        E06_P4
        0.3
        24.1
        92.5%
        56.7%
        91.5%
        E06_P4_S150_R2_001
        20.0%
        52%
        0.3
        E07_P3
        1.0
        95.6
        93.6%
        62.3%
        93.2%
        E07_P3_S55_R2_001
        35.4%
        49%
        1.0
        E07_P4
        5.0
        528.4
        94.2%
        72.9%
        93.4%
        E07_P4_S151_R2_001
        66.3%
        48%
        5.0
        E08_P3
        0.8
        75.9
        93.7%
        64.0%
        93.1%
        E08_P3_S56_R2_001
        40.0%
        49%
        0.8
        E08_P4
        3.4
        359.0
        94.2%
        72.7%
        93.2%
        E08_P4_S152_R2_001
        65.0%
        49%
        3.4
        E09_P3
        0.8
        73.1
        93.5%
        65.3%
        92.8%
        E09_P3_S57_R2_001
        42.0%
        50%
        0.8
        E09_P4
        1.8
        186.7
        93.8%
        72.0%
        92.8%
        E09_P4_S153_R2_001
        60.6%
        49%
        1.8
        E10_P3
        1.0
        99.2
        93.6%
        64.6%
        93.0%
        E10_P3_S58_R2_001
        43.2%
        48%
        1.0
        E10_P4
        1.8
        192.3
        94.7%
        73.6%
        93.8%
        E10_P4_S154_R2_001
        64.0%
        50%
        1.8
        E11_P3
        0.7
        68.7
        93.4%
        65.4%
        92.6%
        E11_P3_S59_R2_001
        44.3%
        49%
        0.7
        E11_P4
        2.1
        227.2
        94.3%
        73.8%
        92.9%
        E11_P4_S155_R2_001
        64.1%
        49%
        2.1
        E12_P3
        0.8
        80.3
        93.6%
        66.4%
        93.5%
        E12_P3_S60_R2_001
        46.4%
        49%
        0.8
        E12_P4
        2.7
        282.9
        94.2%
        72.1%
        93.7%
        E12_P4_S156_R2_001
        62.0%
        50%
        2.7
        F01_P3
        0.8
        80.9
        93.6%
        67.5%
        92.7%
        F01_P3_S61_R2_001
        48.3%
        48%
        0.8
        F01_P4
        7.7
        814.2
        94.4%
        74.1%
        94.2%
        F01_P4_S157_R2_001
        70.9%
        48%
        7.7
        F02_P3
        1.4
        134.2
        93.9%
        66.1%
        91.6%
        F02_P3_S62_R2_001
        47.9%
        49%
        1.4
        F02_P4
        4.5
        468.7
        94.4%
        71.8%
        93.1%
        F02_P4_S158_R2_001
        66.6%
        50%
        4.5
        F03_P3
        0.6
        60.2
        93.0%
        62.3%
        87.2%
        F03_P3_S63_R2_001
        34.7%
        49%
        0.6
        F03_P4
        3.6
        372.7
        94.0%
        72.6%
        88.3%
        F03_P4_S159_R2_001
        65.6%
        48%
        3.6
        F04_P3
        0.6
        63.5
        93.4%
        66.2%
        92.8%
        F04_P3_S64_R2_001
        43.9%
        49%
        0.6
        F04_P4
        3.2
        337.0
        94.1%
        72.5%
        94.1%
        F04_P4_S160_R2_001
        64.4%
        48%
        3.2
        F05_P3
        1.2
        110.5
        93.3%
        63.8%
        92.6%
        F05_P3_S65_R2_001
        39.4%
        49%
        1.2
        F05_P4
        5.8
        614.9
        94.3%
        73.5%
        94.2%
        F05_P4_S161_R2_001
        68.8%
        48%
        5.8
        F06_P3
        0.9
        89.0
        93.6%
        63.9%
        92.4%
        F06_P3_S66_R2_001
        39.2%
        49%
        0.9
        F06_P4
        2.4
        246.1
        94.2%
        72.5%
        93.8%
        F06_P4_S162_R2_001
        64.1%
        48%
        2.4
        F07_P3
        0.8
        74.1
        93.5%
        63.4%
        92.6%
        F07_P3_S67_R2_001
        36.2%
        49%
        0.8
        F07_P4
        6.8
        708.0
        94.1%
        72.3%
        93.9%
        F07_P4_S163_R2_001
        66.5%
        46%
        6.8
        F08_P3
        0.5
        51.3
        93.5%
        65.7%
        92.4%
        F08_P3_S68_R2_001
        43.4%
        49%
        0.5
        F08_P4
        4.7
        494.4
        94.4%
        73.0%
        93.8%
        F08_P4_S164_R2_001
        67.7%
        48%
        4.7
        F09_P3
        0.7
        67.6
        93.2%
        64.0%
        92.1%
        F09_P3_S69_R2_001
        38.7%
        50%
        0.7
        F09_P4
        2.9
        310.9
        94.3%
        73.5%
        93.5%
        F09_P4_S165_R2_001
        65.7%
        49%
        2.9
        F10_P3
        0.7
        63.9
        93.6%
        65.7%
        92.4%
        F10_P3_S70_R2_001
        43.5%
        49%
        0.7
        F10_P4
        1.6
        167.2
        94.6%
        73.0%
        93.9%
        F10_P4_S166_R2_001
        63.5%
        49%
        1.6
        F11_P3
        1.1
        104.4
        92.8%
        61.3%
        91.6%
        F11_P3_S71_R2_001
        32.1%
        49%
        1.1
        F11_P4
        2.1
        221.9
        94.2%
        72.6%
        93.3%
        F11_P4_S167_R2_001
        62.3%
        49%
        2.1
        F12_P3
        0.7
        63.0
        93.3%
        64.9%
        92.8%
        F12_P3_S72_R2_001
        40.9%
        49%
        0.7
        F12_P4
        3.6
        373.1
        94.3%
        72.5%
        94.3%
        F12_P4_S168_R2_001
        65.1%
        49%
        3.6
        G01_P3
        0.8
        74.9
        93.6%
        65.3%
        93.3%
        G01_P3_S73_R2_001
        43.3%
        47%
        0.8
        G01_P4
        5.2
        551.3
        94.3%
        73.6%
        94.0%
        G01_P4_S169_R2_001
        69.2%
        48%
        5.2
        G02_P3
        0.9
        89.8
        93.6%
        63.1%
        92.2%
        G02_P3_S74_R2_001
        40.4%
        48%
        0.9
        G02_P4
        2.7
        272.6
        94.1%
        69.9%
        92.6%
        G02_P4_S170_R2_001
        60.6%
        49%
        2.7
        G03_P3
        0.9
        88.0
        93.5%
        64.6%
        88.5%
        G03_P3_S75_R2_001
        41.7%
        47%
        0.9
        G03_P4
        3.4
        354.2
        94.0%
        72.3%
        88.1%
        G03_P4_S171_R2_001
        64.8%
        48%
        3.4
        G04_P3
        0.6
        62.0
        93.5%
        65.4%
        93.4%
        G04_P3_S76_R2_001
        41.8%
        47%
        0.6
        G04_P4
        3.5
        371.8
        94.2%
        73.3%
        94.2%
        G04_P4_S172_R2_001
        65.7%
        48%
        3.5
        G05_P3
        0.9
        87.2
        93.7%
        66.0%
        93.5%
        G05_P3_S77_R2_001
        45.8%
        47%
        0.9
        G05_P4
        4.5
        468.5
        94.2%
        73.0%
        94.1%
        G05_P4_S173_R2_001
        67.1%
        48%
        4.5
        G06_P3
        0.9
        86.8
        93.9%
        66.9%
        93.2%
        G06_P3_S78_R2_001
        48.2%
        47%
        0.9
        G06_P4
        3.0
        320.5
        94.4%
        73.3%
        93.8%
        G06_P4_S174_R2_001
        66.1%
        48%
        3.0
        G07_P3
        0.6
        58.1
        93.6%
        66.2%
        93.3%
        G07_P3_S79_R2_001
        45.1%
        46%
        0.6
        G07_P4
        5.7
        606.8
        94.5%
        73.8%
        94.0%
        G07_P4_S175_R2_001
        69.2%
        48%
        5.7
        G08_P3
        0.7
        74.0
        93.9%
        67.8%
        93.2%
        G08_P3_S80_R2_001
        50.8%
        47%
        0.7
        G08_P4
        4.2
        438.4
        94.3%
        73.2%
        93.8%
        G08_P4_S176_R2_001
        66.6%
        48%
        4.2
        G09_P3
        0.1
        9.9
        93.2%
        62.3%
        92.3%
        G09_P3_S81_R2_001
        33.7%
        50%
        0.1
        G09_P4
        1.9
        196.7
        94.0%
        72.4%
        93.3%
        G09_P4_S177_R2_001
        62.8%
        49%
        1.9
        G10_P3
        0.8
        74.4
        93.7%
        65.7%
        93.2%
        G10_P3_S82_R2_001
        45.0%
        47%
        0.8
        G10_P4
        2.2
        234.5
        94.6%
        73.7%
        93.9%
        G10_P4_S178_R2_001
        66.6%
        49%
        2.2
        G11_P3
        0.7
        63.5
        93.3%
        63.8%
        92.6%
        G11_P3_S83_R2_001
        38.5%
        47%
        0.7
        G11_P4
        1.6
        162.8
        93.8%
        68.8%
        93.0%
        G11_P4_S179_R2_001
        52.9%
        49%
        1.6
        G12_P3
        0.8
        78.7
        93.6%
        65.8%
        93.5%
        G12_P3_S84_R2_001
        43.7%
        47%
        0.8
        G12_P4
        3.7
        392.2
        94.4%
        73.8%
        94.2%
        G12_P4_S180_R2_001
        68.3%
        48%
        3.7
        H01_P3
        0.8
        77.2
        93.7%
        66.8%
        93.4%
        H01_P3_S85_R2_001
        47.2%
        47%
        0.8
        H01_P4
        5.3
        564.7
        94.4%
        74.0%
        94.7%
        H01_P4_S181_R2_001
        68.8%
        48%
        5.3
        H02_P3
        1.0
        94.5
        93.8%
        65.6%
        92.4%
        H02_P3_S86_R2_001
        47.2%
        49%
        1.0
        H02_P4
        3.2
        338.5
        94.6%
        72.7%
        93.8%
        H02_P4_S182_R2_001
        66.6%
        49%
        3.2
        H03_P3
        0.8
        75.8
        93.4%
        65.7%
        88.4%
        H03_P3_S87_R2_001
        44.8%
        48%
        0.8
        H03_P4
        3.0
        309.4
        93.9%
        72.1%
        88.8%
        H03_P4_S183_R2_001
        62.6%
        48%
        3.0
        H04_P3
        0.6
        63.8
        93.7%
        67.0%
        93.6%
        H04_P3_S88_R2_001
        46.2%
        47%
        0.6
        H04_P4
        3.8
        397.6
        94.3%
        73.4%
        94.7%
        H04_P4_S184_R2_001
        67.0%
        48%
        3.8
        H05_P3
        0.9
        83.6
        93.5%
        64.4%
        93.5%
        H05_P3_S89_R2_001
        40.9%
        47%
        0.9
        H05_P4
        4.0
        426.8
        94.2%
        73.4%
        94.7%
        H05_P4_S185_R2_001
        67.8%
        48%
        4.0
        H06_P3
        0.6
        59.4
        93.8%
        66.1%
        93.2%
        H06_P3_S90_R2_001
        44.8%
        47%
        0.6
        H06_P4
        2.2
        235.1
        94.3%
        73.1%
        94.3%
        H06_P4_S186_R2_001
        64.7%
        48%
        2.2
        H07_P3
        0.2
        14.6
        93.4%
        51.5%
        93.5%
        H07_P3_S91_R2_001
        5.6%
        52%
        0.2
        H07_P4
        4.0
        420.1
        94.7%
        74.1%
        94.6%
        H07_P4_S187_R2_001
        70.0%
        49%
        4.0
        H08_P3
        0.3
        30.6
        93.6%
        62.6%
        93.4%
        H08_P3_S92_R2_001
        34.7%
        49%
        0.3
        H08_P4
        2.1
        222.1
        94.5%
        73.6%
        94.4%
        H08_P4_S188_R2_001
        64.3%
        48%
        2.1
        H09_P3
        0.5
        49.0
        93.5%
        66.4%
        92.9%
        H09_P3_S93_R2_001
        46.4%
        48%
        0.5
        H09_P4
        0.3
        27.4
        93.6%
        71.5%
        92.4%
        H09_P4_S189_R2_001
        60.4%
        47%
        0.3
        H10_P3
        0.6
        62.6
        93.9%
        67.6%
        93.4%
        H10_P3_S94_R2_001
        49.4%
        48%
        0.6
        H10_P4
        1.4
        147.7
        94.5%
        73.0%
        94.4%
        H10_P4_S190_R2_001
        63.0%
        48%
        1.4
        H11_P3
        0.5
        51.2
        93.2%
        65.2%
        92.6%
        H11_P3_S95_R2_001
        43.5%
        47%
        0.5
        H11_P4
        0.2
        17.0
        93.5%
        70.1%
        92.6%
        H11_P4_S191_R2_001
        55.3%
        46%
        0.2
        H12_P3
        0.9
        84.6
        93.8%
        65.6%
        93.6%
        H12_P3_S96_R2_001
        42.3%
        48%
        0.9
        H12_P4
        2.9
        307.5
        94.2%
        73.1%
        94.7%
        H12_P4_S192_R2_001
        67.2%
        48%
        2.9
        undetermined
        108.4
        10137.8
        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (100bp).

        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

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        bcl2fastq

        bcl2fastq can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.

        Lane Statistics

        Statistics about each lane for each flowcell

        Showing 4/4 rows and 5/5 columns.
        Run ID - LaneMb Total YieldM Total Clusters% bases ≥ Q30Mean Quality% Perfect Index
        210127_NS500488_1112_AHG2C7BGXH - L1
        13312.1
        99.3
        76.9%
        30.7
        93.2%
        210127_NS500488_1112_AHG2C7BGXH - L2
        13154.3
        98.2
        77.0%
        30.7
        93.2%
        210127_NS500488_1112_AHG2C7BGXH - L3
        13130.3
        98.0
        75.7%
        30.5
        92.0%
        210127_NS500488_1112_AHG2C7BGXH - L4
        13325.1
        99.4
        77.0%
        30.7
        92.7%

        Clusters by lane

        Number of reads per lane (with number of perfect index reads).

        Perfect index reads are those that do not have a single mismatch. All samples of a lane are combined. Undetermined reads are treated as a third category.

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        Clusters by sample

        Number of reads per sample.

        Perfect index reads are those that do not have a single mismatch. All samples are aggregated across lanes combinned. Undetermined reads are ignored. Undetermined reads are treated as a separate sample.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Undetermined barcodes by lane

        Count of the top twenty most abundant undetermined barcodes by lanes

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