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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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        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 2023-04-24, 17:04 CEST based on data in:

        General Statistics

        Showing 280/280 rows and 13/19 columns.
        Sample Name% Dups% GCM Seqs% DuplicationM Reads After FilteringGC content% PF% AdapterN50 (Kbp)Assembly Length (Mbp)OrganismContigsCDS
        VE19170
        Enterococcus cecorum
        57.0
        2265
        VE19170_1
        43.3%
        36%
        4.7
        VE19170_2
        39.3%
        36%
        4.7
        VE19170_contigs
        183.7Kbp
        2.3Mbp
        VE19170_fastp
        2.6%
        9.2
        36.6%
        98.5%
        2.4%
        VE19205
        Enterococcus cecorum
        60.0
        2319
        VE19205_1
        43.6%
        36%
        5.6
        VE19205_2
        39.3%
        36%
        5.6
        VE19205_contigs
        173.8Kbp
        2.4Mbp
        VE19205_fastp
        2.0%
        11.0
        36.6%
        98.4%
        4.5%
        VE19212
        Enterococcus cecorum
        51.0
        2175
        VE19212_1
        49.8%
        37%
        6.2
        VE19212_2
        47.6%
        37%
        6.2
        VE19212_contigs
        197.4Kbp
        2.2Mbp
        VE19212_fastp
        3.0%
        12.3
        36.8%
        98.7%
        5.3%
        VE19215
        Enterococcus cecorum
        82.0
        2320
        VE19215_1
        49.9%
        37%
        7.4
        VE19215_2
        45.3%
        37%
        7.4
        VE19215_contigs
        169.9Kbp
        2.4Mbp
        VE19215_fastp
        2.1%
        14.5
        36.7%
        98.5%
        5.0%
        VE19223
        Enterococcus cecorum
        53.0
        2044
        VE19223_1
        46.4%
        37%
        5.7
        VE19223_2
        42.5%
        37%
        5.7
        VE19223_contigs
        253.6Kbp
        2.1Mbp
        VE19223_fastp
        2.0%
        11.2
        36.9%
        98.5%
        3.6%
        VE19226
        Enterococcus cecorum
        67.0
        2318
        VE19226_1
        42.3%
        36%
        5.3
        VE19226_2
        39.1%
        37%
        5.3
        VE19226_contigs
        174.4Kbp
        2.4Mbp
        VE19226_fastp
        2.5%
        10.4
        36.8%
        98.7%
        3.7%
        ceco_comA_004_2
        Enterococcus cecorum
        112.0
        2289
        ceco_comA_004_2_1
        45.3%
        36%
        5.3
        ceco_comA_004_2_2
        45.1%
        36%
        5.3
        ceco_comA_004_2_contigs
        119.2Kbp
        2.3Mbp
        ceco_comA_004_2_fastp
        3.4%
        10.4
        36.5%
        98.9%
        3.5%
        ceco_comA_122_1
        Enterococcus cecorum
        161.0
        2317
        ceco_comA_122_1_1
        37.5%
        37%
        3.9
        ceco_comA_122_1_2
        37.0%
        37%
        3.9
        ceco_comA_122_1_contigs
        47.6Kbp
        2.4Mbp
        ceco_comA_122_1_fastp
        3.0%
        7.7
        36.7%
        98.8%
        5.4%
        comA_004_2
        Enterococcus cecorum
        98.0
        2289
        comA_004_2_1
        60.3%
        36%
        11.6
        comA_004_2_2
        55.6%
        36%
        11.6
        comA_004_2_contigs
        119.2Kbp
        2.3Mbp
        comA_004_2_fastp
        2.4%
        22.7
        36.3%
        98.3%
        6.0%
        comA_122_1
        Enterococcus cecorum
        168.0
        2314
        comA_122_1_1
        58.2%
        37%
        11.0
        comA_122_1_2
        52.3%
        37%
        11.0
        comA_122_1_contigs
        45.4Kbp
        2.4Mbp
        comA_122_1_fastp
        1.7%
        21.6
        36.7%
        98.2%
        5.5%
        comA_155_1
        Enterococcus cecorum
        166.0
        2215
        comA_155_1_1
        50.1%
        37%
        7.5
        comA_155_1_2
        44.7%
        37%
        7.5
        comA_155_1_contigs
        49.1Kbp
        2.3Mbp
        comA_155_1_fastp
        1.2%
        14.8
        36.9%
        98.2%
        5.6%
        comA_159_1
        Enterococcus cecorum
        79.0
        2113
        comA_159_1_1
        58.6%
        37%
        11.0
        comA_159_1_2
        53.0%
        37%
        11.0
        comA_159_1_contigs
        210.5Kbp
        2.2Mbp
        comA_159_1_fastp
        1.6%
        21.6
        36.7%
        98.1%
        6.8%
        comA_164_1
        Enterococcus cecorum
        1380.0
        2503
        comA_164_1_1
        57.3%
        36%
        11.3
        comA_164_1_2
        55.1%
        36%
        11.3
        comA_164_1_contigs
        80.5Kbp
        2.5Mbp
        comA_164_1_fastp
        1.8%
        22.2
        36.6%
        98.5%
        6.4%
        comA_171_1
        Enterococcus cecorum
        1644.0
        4647
        comA_171_1_1
        49.5%
        35%
        8.4
        comA_171_1_2
        46.6%
        35%
        8.4
        comA_171_1_contigs
        13.4Kbp
        4.7Mbp
        comA_171_1_fastp
        1.4%
        16.7
        35.1%
        98.6%
        4.5%
        comA_173_1
        Enterococcus cecorum
        151.0
        2430
        comA_173_1_1
        53.5%
        36%
        9.3
        comA_173_1_2
        46.4%
        36%
        9.3
        comA_173_1_contigs
        80.0Kbp
        2.5Mbp
        comA_173_1_fastp
        1.5%
        18.4
        36.1%
        98.2%
        5.9%
        comA_175_1
        Enterococcus cecorum
        111.0
        2518
        comA_175_1_1
        52.8%
        36%
        9.9
        comA_175_1_2
        46.8%
        36%
        9.9
        comA_175_1_contigs
        137.4Kbp
        2.6Mbp
        comA_175_1_fastp
        1.5%
        19.4
        36.4%
        98.3%
        4.5%
        comA_177_1
        Enterococcus cecorum
        3599.0
        4409
        comA_177_1_1
        42.3%
        37%
        5.5
        comA_177_1_2
        43.4%
        37%
        5.5
        comA_177_1_contigs
        28.5Kbp
        4.5Mbp
        comA_177_1_fastp
        4.3%
        11.0
        37.1%
        99.0%
        4.8%
        comA_178_1
        Enterococcus cecorum
        97.0
        2524
        comA_178_1_1
        56.4%
        36%
        11.6
        comA_178_1_2
        51.9%
        36%
        11.6
        comA_178_1_contigs
        137.4Kbp
        2.6Mbp
        comA_178_1_fastp
        1.9%
        22.7
        36.3%
        98.2%
        6.7%
        comA_180_3
        Enterococcus cecorum
        180.0
        2416
        comA_180_3_1
        54.7%
        37%
        10.1
        comA_180_3_2
        49.6%
        37%
        10.1
        comA_180_3_contigs
        94.6Kbp
        2.5Mbp
        comA_180_3_fastp
        1.3%
        19.8
        36.5%
        98.2%
        6.7%
        comA_184_4
        Enterococcus cecorum
        105.0
        2305
        comA_184_4_1
        59.5%
        37%
        12.0
        comA_184_4_2
        56.0%
        37%
        12.0
        comA_184_4_contigs
        110.9Kbp
        2.4Mbp
        comA_184_4_fastp
        1.7%
        23.7
        36.7%
        98.6%
        6.2%
        comA_193_1
        Enterococcus cecorum
        310.0
        2394
        comA_193_1_1
        48.4%
        36%
        7.4
        comA_193_1_2
        44.5%
        37%
        7.4
        comA_193_1_contigs
        107.3Kbp
        2.5Mbp
        comA_193_1_fastp
        1.4%
        14.6
        36.6%
        98.5%
        5.7%
        comA_200_1
        Enterococcus cecorum
        126.0
        2453
        comA_200_1_1
        47.8%
        36%
        7.3
        comA_200_1_2
        44.0%
        36%
        7.3
        comA_200_1_contigs
        120.1Kbp
        2.5Mbp
        comA_200_1_fastp
        1.2%
        14.4
        36.5%
        98.4%
        4.8%
        comA_221_1
        Enterococcus cecorum
        77.0
        2251
        comA_221_1_1
        50.7%
        36%
        8.0
        comA_221_1_2
        42.5%
        37%
        8.0
        comA_221_1_contigs
        140.7Kbp
        2.3Mbp
        comA_221_1_fastp
        1.2%
        15.6
        36.7%
        98.0%
        4.5%
        comA_224_1
        Enterococcus cecorum
        74.0
        2346
        comA_224_1_1
        49.0%
        37%
        7.6
        comA_224_1_2
        41.5%
        37%
        7.6
        comA_224_1_contigs
        135.7Kbp
        2.4Mbp
        comA_224_1_fastp
        1.1%
        14.9
        36.6%
        97.8%
        5.1%
        comA_225_1
        Enterococcus cecorum
        106.0
        2388
        comA_225_1_1
        55.1%
        36%
        10.4
        comA_225_1_2
        50.9%
        36%
        10.4
        comA_225_1_contigs
        187.3Kbp
        2.5Mbp
        comA_225_1_fastp
        1.7%
        20.5
        36.5%
        98.4%
        5.4%
        comA_229_2
        Enterococcus cecorum
        100.0
        2375
        comA_229_2_1
        60.0%
        36%
        12.3
        comA_229_2_2
        53.7%
        36%
        12.3
        comA_229_2_contigs
        126.8Kbp
        2.4Mbp
        comA_229_2_fastp
        1.6%
        24.2
        36.5%
        98.3%
        5.2%
        comA_234_1
        Enterococcus cecorum
        95.0
        2501
        comA_234_1_1
        50.0%
        37%
        8.7
        comA_234_1_2
        45.8%
        37%
        8.7
        comA_234_1_contigs
        89.9Kbp
        2.6Mbp
        comA_234_1_fastp
        1.4%
        17.1
        36.7%
        98.3%
        6.7%
        comA_235_1
        Enterococcus cecorum
        336.0
        2505
        comA_235_1_1
        52.2%
        36%
        9.7
        comA_235_1_2
        47.4%
        37%
        9.7
        comA_235_1_contigs
        162.8Kbp
        2.6Mbp
        comA_235_1_fastp
        1.5%
        18.9
        36.5%
        98.0%
        5.5%
        comA_236_1
        Enterococcus cecorum
        96.0
        2172
        comA_236_1_1
        60.4%
        36%
        11.8
        comA_236_1_2
        53.8%
        37%
        11.8
        comA_236_1_contigs
        93.4Kbp
        2.3Mbp
        comA_236_1_fastp
        1.7%
        23.1
        36.6%
        98.3%
        4.9%
        comA_237_1
        Enterococcus cecorum
        82.0
        2173
        comA_237_1_1
        49.0%
        36%
        7.1
        comA_237_1_2
        43.7%
        36%
        7.1
        comA_237_1_contigs
        98.0Kbp
        2.3Mbp
        comA_237_1_fastp
        1.2%
        14.0
        36.6%
        98.4%
        4.0%
        comA_243_1
        Enterococcus cecorum
        2195.0
        4576
        comA_243_1_1
        36.8%
        38%
        4.6
        comA_243_1_2
        43.3%
        38%
        4.6
        comA_243_1_contigs
        55.3Kbp
        4.8Mbp
        comA_243_1_fastp
        2.9%
        9.1
        38.2%
        98.9%
        4.7%
        comA_246_1
        Enterococcus cecorum
        158.0
        2469
        comA_246_1_1
        55.4%
        36%
        10.4
        comA_246_1_2
        48.5%
        36%
        10.4
        comA_246_1_contigs
        95.7Kbp
        2.5Mbp
        comA_246_1_fastp
        1.6%
        20.4
        36.3%
        98.1%
        5.1%
        comA_252_1
        Enterococcus cecorum
        327.0
        2415
        comA_252_1_1
        49.8%
        36%
        8.3
        comA_252_1_2
        46.2%
        36%
        8.3
        comA_252_1_contigs
        126.8Kbp
        2.5Mbp
        comA_252_1_fastp
        1.4%
        16.3
        36.4%
        98.4%
        4.9%
        comA_262_1
        Enterococcus cecorum
        177.0
        2133
        comA_262_1_1
        45.3%
        36%
        5.3
        comA_262_1_2
        42.7%
        37%
        5.3
        comA_262_1_contigs
        47.9Kbp
        2.2Mbp
        comA_262_1_fastp
        2.7%
        10.4
        36.7%
        98.6%
        4.5%
        comA_264_1
        Enterococcus cecorum
        98.0
        2410
        comA_264_1_1
        48.7%
        37%
        7.0
        comA_264_1_2
        45.8%
        37%
        7.0
        comA_264_1_contigs
        163.0Kbp
        2.5Mbp
        comA_264_1_fastp
        2.6%
        13.9
        36.8%
        98.8%
        3.9%
        comA_267_1
        Enterococcus cecorum
        171.0
        2373
        comA_267_1_1
        42.6%
        36%
        5.1
        comA_267_1_2
        39.4%
        37%
        5.1
        comA_267_1_contigs
        52.0Kbp
        2.4Mbp
        comA_267_1_fastp
        2.3%
        10.1
        36.7%
        98.6%
        3.4%
        comA_83_2
        Enterococcus cecorum
        1400.0
        4527
        comA_83_2_1
        52.4%
        37%
        10.2
        comA_83_2_2
        47.7%
        38%
        10.2
        comA_83_2_contigs
        11.1Kbp
        4.7Mbp
        comA_83_2_fastp
        1.7%
        20.1
        37.5%
        98.2%
        6.1%
        comA_87_1
        Enterococcus cecorum
        152.0
        2213
        comA_87_1_1
        55.6%
        37%
        9.6
        comA_87_1_2
        50.1%
        37%
        9.6
        comA_87_1_contigs
        53.8Kbp
        2.3Mbp
        comA_87_1_fastp
        1.5%
        18.9
        36.8%
        98.2%
        5.6%
        comI_002
        Enterococcus cecorum
        77.0
        2118
        comI_002_1
        46.0%
        37%
        5.5
        comI_002_2
        42.0%
        37%
        5.5
        comI_002_contigs
        147.9Kbp
        2.2Mbp
        comI_002_fastp
        2.2%
        10.9
        36.9%
        98.8%
        3.2%
        comI_118_1
        Enterococcus cecorum
        194.0
        2248
        comI_118_1_1
        45.1%
        36%
        5.6
        comI_118_1_2
        43.0%
        36%
        5.6
        comI_118_1_contigs
        38.4Kbp
        2.3Mbp
        comI_118_1_fastp
        2.2%
        11.1
        36.6%
        98.8%
        4.0%
        comI_122_1
        Enterococcus cecorum
        162.0
        2404
        comI_122_1_1
        44.5%
        37%
        5.9
        comI_122_1_2
        40.4%
        37%
        5.9
        comI_122_1_contigs
        58.7Kbp
        2.5Mbp
        comI_122_1_fastp
        2.0%
        11.6
        36.7%
        98.4%
        4.8%
        comI_154_2
        Enterococcus cecorum
        53.0
        2701
        comI_154_2_1
        40.7%
        37%
        5.4
        comI_154_2_2
        36.1%
        37%
        5.4
        comI_154_2_contigs
        279.8Kbp
        2.9Mbp
        comI_154_2_fastp
        2.1%
        10.6
        37.4%
        98.1%
        3.8%
        comI_156_1
        Enterococcus cecorum
        3441.0
        3884
        comI_156_1_1
        52.7%
        36%
        6.8
        comI_156_1_2
        50.0%
        36%
        6.8
        comI_156_1_contigs
        84.4Kbp
        3.8Mbp
        comI_156_1_fastp
        4.7%
        13.5
        36.3%
        98.8%
        4.6%
        comI_183_1
        Enterococcus cecorum
        2133.0
        3362
        comI_183_1_1
        49.8%
        36%
        6.7
        comI_183_1_2
        48.0%
        36%
        6.7
        comI_183_1_contigs
        101.6Kbp
        3.3Mbp
        comI_183_1_fastp
        4.4%
        13.3
        36.6%
        98.9%
        3.8%
        comI_191_2
        Enterococcus cecorum
        2958.0
        4119
        comI_191_2_1
        45.9%
        37%
        7.8
        comI_191_2_2
        44.0%
        37%
        7.8
        comI_191_2_contigs
        148.9Kbp
        4.3Mbp
        comI_191_2_fastp
        2.9%
        15.4
        37.4%
        98.5%
        6.0%
        comI_197_5
        Enterococcus cecorum
        112.0
        2417
        comI_197_5_1
        52.1%
        36%
        7.9
        comI_197_5_2
        49.4%
        36%
        7.9
        comI_197_5_contigs
        113.1Kbp
        2.5Mbp
        comI_197_5_fastp
        2.8%
        15.7
        36.6%
        98.7%
        4.7%
        comI_201_1
        Enterococcus cecorum
        112.0
        2461
        comI_201_1_1
        43.8%
        36%
        5.3
        comI_201_1_2
        41.4%
        36%
        5.3
        comI_201_1_contigs
        116.2Kbp
        2.5Mbp
        comI_201_1_fastp
        2.5%
        10.4
        36.3%
        98.5%
        3.8%
        comI_244_3
        Enterococcus cecorum
        428.0
        3038
        comI_244_3_1
        47.1%
        37%
        6.9
        comI_244_3_2
        45.1%
        37%
        6.9
        comI_244_3_contigs
        84.4Kbp
        3.2Mbp
        comI_244_3_fastp
        2.8%
        13.6
        36.9%
        98.8%
        3.8%
        comI_250_1
        Enterococcus cecorum
        80.0
        2217
        comI_250_1_1
        45.1%
        36%
        5.1
        comI_250_1_2
        41.2%
        36%
        5.1
        comI_250_1_contigs
        148.0Kbp
        2.3Mbp
        comI_250_1_fastp
        2.4%
        10.2
        36.6%
        98.6%
        3.5%
        comI_252_1
        Enterococcus cecorum
        131.0
        2405
        comI_252_1_1
        49.9%
        36%
        7.5
        comI_252_1_2
        47.0%
        36%
        7.5
        comI_252_1_contigs
        126.8Kbp
        2.5Mbp
        comI_252_1_fastp
        2.6%
        14.7
        36.4%
        98.6%
        3.6%
        comI_255_1
        Enterococcus cecorum
        169.0
        2389
        comI_255_1_1
        50.5%
        36%
        7.4
        comI_255_1_2
        46.8%
        36%
        7.4
        comI_255_1_contigs
        89.5Kbp
        2.4Mbp
        comI_255_1_fastp
        2.4%
        14.6
        36.4%
        98.6%
        4.1%
        comI_264_1
        Enterococcus cecorum
        100.0
        2412
        comI_264_1_1
        43.2%
        37%
        5.6
        comI_264_1_2
        40.8%
        37%
        5.6
        comI_264_1_contigs
        163.0Kbp
        2.5Mbp
        comI_264_1_fastp
        2.6%
        11.1
        36.8%
        98.8%
        4.0%
        comI_265_1
        Enterococcus cecorum
        73.0
        2293
        comI_265_1_1
        42.8%
        36%
        4.9
        comI_265_1_2
        39.6%
        36%
        4.9
        comI_265_1_contigs
        120.2Kbp
        2.4Mbp
        comI_265_1_fastp
        3.0%
        9.6
        36.5%
        98.6%
        3.0%
        comI_266_1
        Enterococcus cecorum
        78.0
        2202
        comI_266_1_1
        48.0%
        36%
        6.3
        comI_266_1_2
        45.4%
        37%
        6.3
        comI_266_1_contigs
        123.8Kbp
        2.3Mbp
        comI_266_1_fastp
        2.5%
        12.5
        36.8%
        98.7%
        3.0%
        comI_82_2
        Enterococcus cecorum
        180.0
        2707
        comI_82_2_1
        47.8%
        36%
        6.7
        comI_82_2_2
        45.6%
        36%
        6.7
        comI_82_2_contigs
        98.7Kbp
        2.7Mbp
        comI_82_2_fastp
        2.5%
        13.2
        36.5%
        98.8%
        3.9%
        comI_94_1
        Enterococcus cecorum
        169.0
        2212
        comI_94_1_1
        48.2%
        37%
        6.3
        comI_94_1_2
        45.3%
        37%
        6.3
        comI_94_1_contigs
        53.8Kbp
        2.3Mbp
        comI_94_1_fastp
        2.3%
        12.4
        36.9%
        98.6%
        3.9%

        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 (151bp).

        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.

        112 samples had less than 1% of reads made up of overrepresented sequences

        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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        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.

        Filtered Reads

        Filtering statistics of sampled reads.

        loading..

        Insert Sizes

        Insert size estimation of sampled reads.

        loading..

        Sequence Quality

        Average sequencing quality over each base of all reads.

        loading..

        GC Content

        Average GC content over each base of all reads.

        loading..

        N content

        Average N content over each base of all reads.

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        QUAST

        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.DOI: 10.1093/bioinformatics/btt086.

        Assembly Statistics

        Showing 56/56 rows and 8/8 columns.
        Sample NameN50 (Kbp)L50 (K)Largest contig (Kbp)Length (Mbp)MisassembliesMismatches/100kbpIndels/100kbpGenome Fraction
        VE19170_contigs
        183.7Kbp
        0.0K
        478.3Kbp
        2.3Mbp
        71.0
        1833.77
        69.28
        80.8%
        VE19205_contigs
        173.8Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        71.0
        3355.65
        120.40
        68.8%
        VE19212_contigs
        197.4Kbp
        0.0K
        635.7Kbp
        2.2Mbp
        72.0
        1857.94
        68.14
        79.6%
        VE19215_contigs
        169.9Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        71.0
        3358.26
        121.12
        68.7%
        VE19223_contigs
        253.6Kbp
        0.0K
        341.1Kbp
        2.1Mbp
        78.0
        1909.37
        63.43
        75.8%
        VE19226_contigs
        174.4Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        64.0
        3344.02
        119.15
        68.6%
        ceco_comA_004_2_contigs
        119.2Kbp
        0.0K
        280.5Kbp
        2.3Mbp
        56.0
        1331.56
        49.04
        80.5%
        ceco_comA_122_1_contigs
        47.6Kbp
        0.0K
        124.7Kbp
        2.4Mbp
        78.0
        1907.89
        70.87
        75.6%
        comA_004_2_contigs
        119.2Kbp
        0.0K
        280.5Kbp
        2.3Mbp
        57.0
        1331.73
        48.93
        80.5%
        comA_122_1_contigs
        45.4Kbp
        0.0K
        124.7Kbp
        2.4Mbp
        76.0
        1912.48
        71.36
        75.6%
        comA_155_1_contigs
        49.1Kbp
        0.0K
        134.1Kbp
        2.3Mbp
        78.0
        2031.83
        75.41
        76.0%
        comA_159_1_contigs
        210.5Kbp
        0.0K
        437.5Kbp
        2.2Mbp
        65.0
        1324.38
        49.75
        81.4%
        comA_164_1_contigs
        80.5Kbp
        0.0K
        201.2Kbp
        2.5Mbp
        39.0
        1132.30
        50.03
        83.8%
        comA_171_1_contigs
        13.4Kbp
        0.0K
        221.7Kbp
        4.7Mbp
        34.0
        996.57
        34.63
        73.8%
        comA_173_1_contigs
        80.0Kbp
        0.0K
        187.5Kbp
        2.5Mbp
        54.0
        1226.47
        45.25
        84.4%
        comA_175_1_contigs
        137.4Kbp
        0.0K
        557.0Kbp
        2.6Mbp
        53.0
        1021.72
        42.54
        85.1%
        comA_177_1_contigs
        28.5Kbp
        0.0K
        534.8Kbp
        4.5Mbp
        52.0
        1035.36
        43.37
        85.4%
        comA_178_1_contigs
        137.4Kbp
        0.0K
        556.8Kbp
        2.6Mbp
        52.0
        1022.11
        42.55
        85.3%
        comA_180_3_contigs
        94.6Kbp
        0.0K
        519.7Kbp
        2.5Mbp
        45.0
        1034.13
        41.78
        85.6%
        comA_184_4_contigs
        110.9Kbp
        0.0K
        205.4Kbp
        2.4Mbp
        57.0
        1214.06
        45.25
        84.1%
        comA_193_1_contigs
        107.3Kbp
        0.0K
        227.2Kbp
        2.5Mbp
        59.0
        1221.76
        46.20
        84.9%
        comA_200_1_contigs
        120.1Kbp
        0.0K
        367.3Kbp
        2.5Mbp
        48.0
        1011.59
        40.40
        84.6%
        comA_221_1_contigs
        140.7Kbp
        0.0K
        379.2Kbp
        2.3Mbp
        65.0
        1207.25
        45.84
        82.6%
        comA_224_1_contigs
        135.7Kbp
        0.0K
        322.4Kbp
        2.4Mbp
        58.0
        1231.31
        46.50
        84.4%
        comA_225_1_contigs
        187.3Kbp
        0.0K
        300.0Kbp
        2.5Mbp
        56.0
        1206.26
        43.82
        84.4%
        comA_229_2_contigs
        126.8Kbp
        0.0K
        280.5Kbp
        2.4Mbp
        52.0
        1204.70
        43.43
        84.2%
        comA_234_1_contigs
        89.9Kbp
        0.0K
        349.9Kbp
        2.6Mbp
        55.0
        1212.54
        45.54
        84.5%
        comA_235_1_contigs
        162.8Kbp
        0.0K
        458.3Kbp
        2.6Mbp
        62.0
        1211.57
        46.21
        84.5%
        comA_236_1_contigs
        93.4Kbp
        0.0K
        266.3Kbp
        2.3Mbp
        61.0
        1327.01
        53.40
        82.1%
        comA_237_1_contigs
        98.0Kbp
        0.0K
        266.7Kbp
        2.3Mbp
        60.0
        1324.12
        53.42
        82.4%
        comA_243_1_contigs
        55.3Kbp
        0.0K
        290.7Kbp
        4.8Mbp
        28.0
        1111.05
        33.55
        62.4%
        comA_246_1_contigs
        95.7Kbp
        0.0K
        334.3Kbp
        2.5Mbp
        53.0
        1009.52
        40.80
        84.7%
        comA_252_1_contigs
        126.8Kbp
        0.0K
        327.6Kbp
        2.5Mbp
        51.0
        1207.50
        43.32
        84.3%
        comA_262_1_contigs
        47.9Kbp
        0.0K
        151.1Kbp
        2.2Mbp
        81.0
        1990.44
        72.27
        74.3%
        comA_264_1_contigs
        163.0Kbp
        0.0K
        300.9Kbp
        2.5Mbp
        54.0
        1199.03
        42.48
        84.0%
        comA_267_1_contigs
        52.0Kbp
        0.0K
        144.0Kbp
        2.4Mbp
        78.0
        2118.93
        78.65
        73.9%
        comA_83_2_contigs
        11.1Kbp
        0.1K
        90.3Kbp
        4.7Mbp
        58.0
        1888.98
        67.33
        68.3%
        comA_87_1_contigs
        53.8Kbp
        0.0K
        169.8Kbp
        2.3Mbp
        82.0
        2043.66
        75.91
        76.0%
        comI_002_contigs
        147.9Kbp
        0.0K
        256.0Kbp
        2.2Mbp
        59.0
        1354.32
        49.52
        80.6%
        comI_118_1_contigs
        38.4Kbp
        0.0K
        120.0Kbp
        2.3Mbp
        73.0
        1998.30
        72.02
        74.9%
        comI_122_1_contigs
        58.7Kbp
        0.0K
        144.5Kbp
        2.5Mbp
        85.0
        2046.22
        77.63
        75.5%
        comI_154_2_contigs
        279.8Kbp
        0.0K
        551.9Kbp
        2.9Mbp
        0.0
        1427.30
        89.21
        0.0%
        comI_156_1_contigs
        84.4Kbp
        0.0K
        431.0Kbp
        3.8Mbp
        1.0
        1116.70
        178.49
        0.9%
        comI_183_1_contigs
        101.6Kbp
        0.0K
        283.7Kbp
        3.3Mbp
        9.0
        1099.28
        51.83
        7.9%
        comI_191_2_contigs
        148.9Kbp
        0.0K
        606.8Kbp
        4.3Mbp
        32.0
        1104.43
        30.39
        47.6%
        comI_197_5_contigs
        113.1Kbp
        0.0K
        280.5Kbp
        2.5Mbp
        57.0
        1234.62
        46.22
        84.4%
        comI_201_1_contigs
        116.2Kbp
        0.0K
        539.3Kbp
        2.5Mbp
        49.0
        1007.99
        40.26
        84.8%
        comI_244_3_contigs
        84.4Kbp
        0.0K
        373.5Kbp
        3.2Mbp
        2.0
        1062.41
        145.05
        1.0%
        comI_250_1_contigs
        148.0Kbp
        0.0K
        311.5Kbp
        2.3Mbp
        61.0
        1205.98
        45.33
        82.4%
        comI_252_1_contigs
        126.8Kbp
        0.0K
        327.7Kbp
        2.5Mbp
        48.0
        1208.07
        43.71
        84.0%
        comI_255_1_contigs
        89.5Kbp
        0.0K
        183.6Kbp
        2.4Mbp
        56.0
        1135.30
        42.00
        83.6%
        comI_264_1_contigs
        163.0Kbp
        0.0K
        375.9Kbp
        2.5Mbp
        56.0
        1199.72
        42.77
        84.2%
        comI_265_1_contigs
        120.2Kbp
        0.0K
        355.6Kbp
        2.4Mbp
        56.0
        1231.87
        46.52
        84.3%
        comI_266_1_contigs
        123.8Kbp
        0.0K
        250.9Kbp
        2.3Mbp
        58.0
        1208.17
        45.36
        82.0%
        comI_82_2_contigs
        98.7Kbp
        0.0K
        190.8Kbp
        2.7Mbp
        60.0
        1393.10
        52.84
        82.2%
        comI_94_1_contigs
        53.8Kbp
        0.0K
        134.2Kbp
        2.3Mbp
        84.0
        2035.15
        75.16
        75.8%

        Number of Contigs

        This plot shows the number of contigs found for each assembly, broken down by length.

        loading..

        Prokka

        Prokka is a software tool for the rapid annotation of prokaryotic genomes.DOI: 10.1093/bioinformatics/btu153.

        This barplot shows the distribution of different types of features found in each contig.

        Prokka can detect different features:

        • CDS
        • rRNA
        • tmRNA
        • tRNA
        • miscRNA
        • signal peptides
        • CRISPR arrays

        This barplot shows you the distribution of these different types of features found in each contig.

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

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