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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 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 2024-01-15, 16:57 CET based on data in:

        General Statistics

        Showing 236/236 rows and 13/19 columns.
        Sample Name% Dups% GCM Seqs% DuplicationM Reads After FilteringGC content% PF% AdapterN50 (Kbp)Assembly Length (Mbp)OrganismContigsCDS
        VE19170
        2.6%
        9.2
        36.6%
        98.5%
        2.4%
        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
        VE19205
        2.0%
        11.0
        36.6%
        98.4%
        4.5%
        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
        VE19212
        3.0%
        12.3
        36.8%
        98.7%
        5.3%
        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
        VE19215
        2.1%
        14.5
        36.7%
        98.5%
        5.0%
        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
        VE19223
        2.0%
        11.2
        36.9%
        98.5%
        3.6%
        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
        VE19226
        2.5%
        10.4
        36.8%
        98.7%
        3.7%
        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
        VE19243
        4.2%
        11.9
        36.8%
        99.3%
        3.2%
        Enterococcus cecorum
        63.0
        2118
        VE19243_1
        48.4%
        36%
        6.0
        VE19243_2
        47.1%
        36%
        6.0
        VE19243_contigs
        252.4Kbp
        2.2Mbp
        VE19244
        7.2%
        10.9
        37.5%
        99.5%
        2.4%
        Enterococcus cecorum
        100.0
        2178
        VE19244_1
        50.0%
        37%
        5.5
        VE19244_2
        54.7%
        37%
        5.5
        VE19244_contigs
        120.0Kbp
        2.3Mbp
        VE19245
        5.5%
        15.4
        36.2%
        99.2%
        3.6%
        Enterococcus cecorum
        59.0
        2289
        VE19245_1
        50.7%
        36%
        7.8
        VE19245_2
        48.6%
        36%
        7.8
        VE19245_contigs
        161.5Kbp
        2.4Mbp
        VE19246
        5.1%
        9.8
        36.6%
        99.4%
        3.4%
        Enterococcus cecorum
        57.0
        2170
        VE19246_1
        45.9%
        36%
        4.9
        VE19246_2
        43.1%
        36%
        4.9
        VE19246_contigs
        110.0Kbp
        2.2Mbp
        VE19247
        4.9%
        10.5
        36.2%
        99.3%
        3.0%
        Enterococcus cecorum
        49.0
        2203
        VE19247_1
        47.0%
        36%
        5.3
        VE19247_2
        45.9%
        36%
        5.3
        VE19247_contigs
        140.0Kbp
        2.3Mbp
        VE19248
        5.3%
        9.2
        36.3%
        99.1%
        4.0%
        Enterococcus cecorum
        81.0
        2202
        VE19248_1
        41.6%
        36%
        4.7
        VE19248_2
        40.2%
        36%
        4.7
        VE19248_contigs
        137.9Kbp
        2.3Mbp
        VE19249
        5.4%
        10.2
        36.4%
        99.1%
        3.3%
        Enterococcus cecorum
        67.0
        2143
        VE19249_1
        46.0%
        36%
        5.2
        VE19249_2
        43.8%
        36%
        5.2
        VE19249_contigs
        96.0Kbp
        2.2Mbp
        VE19250
        3.4%
        10.4
        36.5%
        98.9%
        3.5%
        Enterococcus cecorum
        112.0
        2289
        VE19250_1
        45.3%
        36%
        5.3
        VE19250_2
        45.1%
        36%
        5.3
        VE19250_contigs
        119.2Kbp
        2.3Mbp
        VE19251
        1.7%
        21.6
        36.7%
        98.2%
        5.5%
        Enterococcus cecorum
        168.0
        2314
        VE19251_1
        58.2%
        37%
        11.0
        VE19251_2
        52.3%
        37%
        11.0
        VE19251_contigs
        45.4Kbp
        2.4Mbp
        VE19252
        2.4%
        9.4
        36.4%
        98.6%
        3.6%
        Enterococcus cecorum
        135.0
        2216
        VE19252_1
        41.6%
        36%
        4.7
        VE19252_2
        34.9%
        36%
        4.7
        VE19252_contigs
        48.8Kbp
        2.3Mbp
        VE19253
        1.6%
        21.6
        36.7%
        98.1%
        6.8%
        Enterococcus cecorum
        79.0
        2113
        VE19253_1
        58.6%
        37%
        11.0
        VE19253_2
        53.0%
        37%
        11.0
        VE19253_contigs
        210.5Kbp
        2.2Mbp
        VE19255
        4.6%
        9.0
        36.4%
        99.1%
        4.3%
        Enterococcus cecorum
        985.0
        2440
        VE19255_1
        39.4%
        36%
        4.5
        VE19255_2
        37.3%
        36%
        4.5
        VE19255_contigs
        143.4Kbp
        2.8Mbp
        VE19256
        1.5%
        18.4
        36.1%
        98.2%
        5.9%
        Enterococcus cecorum
        151.0
        2430
        VE19256_1
        53.5%
        36%
        9.3
        VE19256_2
        46.4%
        36%
        9.3
        VE19256_contigs
        80.0Kbp
        2.5Mbp
        VE19257
        1.5%
        19.4
        36.4%
        98.3%
        4.5%
        Enterococcus cecorum
        111.0
        2518
        VE19257_1
        52.8%
        36%
        9.9
        VE19257_2
        46.8%
        36%
        9.9
        VE19257_contigs
        137.4Kbp
        2.6Mbp
        VE19258
        4.4%
        15.1
        35.5%
        99.1%
        5.4%
        Enterococcus cecorum
        206.0
        2507
        VE19258_1
        46.4%
        35%
        7.6
        VE19258_2
        43.5%
        35%
        7.6
        VE19258_contigs
        133.2Kbp
        2.6Mbp
        VE19259
        1.9%
        22.7
        36.3%
        98.2%
        6.7%
        Enterococcus cecorum
        97.0
        2524
        VE19259_1
        56.4%
        36%
        11.6
        VE19259_2
        51.9%
        36%
        11.6
        VE19259_contigs
        137.4Kbp
        2.6Mbp
        VE19260
        5.4%
        15.5
        36.0%
        99.3%
        4.0%
        Enterococcus cecorum
        90.0
        2405
        VE19260_1
        49.8%
        36%
        7.8
        VE19260_2
        48.5%
        36%
        7.8
        VE19260_contigs
        94.6Kbp
        2.5Mbp
        VE19261
        1.7%
        23.7
        36.7%
        98.6%
        6.2%
        Enterococcus cecorum
        105.0
        2305
        VE19261_1
        59.5%
        37%
        12.0
        VE19261_2
        56.0%
        37%
        12.0
        VE19261_contigs
        110.9Kbp
        2.4Mbp
        VE19262
        1.4%
        14.6
        36.6%
        98.5%
        5.7%
        Enterococcus cecorum
        310.0
        2394
        VE19262_1
        48.4%
        36%
        7.4
        VE19262_2
        44.5%
        37%
        7.4
        VE19262_contigs
        98.7Kbp
        2.5Mbp
        VE19263
        1.2%
        14.4
        36.5%
        98.4%
        4.8%
        Enterococcus cecorum
        126.0
        2453
        VE19263_1
        47.8%
        36%
        7.3
        VE19263_2
        44.0%
        36%
        7.3
        VE19263_contigs
        116.2Kbp
        2.5Mbp
        VE19264
        1.2%
        15.6
        36.7%
        98.0%
        4.5%
        Enterococcus cecorum
        77.0
        2251
        VE19264_1
        50.7%
        36%
        8.0
        VE19264_2
        42.5%
        37%
        8.0
        VE19264_contigs
        140.7Kbp
        2.3Mbp
        VE19265
        1.1%
        14.9
        36.6%
        97.8%
        5.1%
        Enterococcus cecorum
        74.0
        2346
        VE19265_1
        49.0%
        37%
        7.6
        VE19265_2
        41.5%
        37%
        7.6
        VE19265_contigs
        135.7Kbp
        2.4Mbp
        VE19266
        1.7%
        20.5
        36.5%
        98.4%
        5.4%
        Enterococcus cecorum
        106.0
        2388
        VE19266_1
        55.1%
        36%
        10.4
        VE19266_2
        50.9%
        36%
        10.4
        VE19266_contigs
        187.3Kbp
        2.5Mbp
        VE19267
        4.5%
        9.3
        36.9%
        99.1%
        3.5%
        Enterococcus cecorum
        880.0
        2250
        VE19267_1
        42.9%
        37%
        4.7
        VE19267_2
        42.1%
        37%
        4.7
        VE19267_contigs
        44.7Kbp
        2.6Mbp
        VE19268
        4.5%
        9.2
        36.4%
        99.1%
        3.5%
        Enterococcus cecorum
        139.0
        2210
        VE19268_1
        41.8%
        36%
        4.7
        VE19268_2
        40.2%
        36%
        4.7
        VE19268_contigs
        53.8Kbp
        2.3Mbp
        VE19269
        1.6%
        24.2
        36.5%
        98.3%
        5.2%
        Enterococcus cecorum
        100.0
        2375
        VE19269_1
        60.0%
        36%
        12.3
        VE19269_2
        53.7%
        36%
        12.3
        VE19269_contigs
        126.8Kbp
        2.4Mbp
        VE19270
        5.0%
        9.0
        36.4%
        99.2%
        2.8%
        Enterococcus cecorum
        75.0
        2502
        VE19270_1
        40.2%
        36%
        4.5
        VE19270_2
        38.7%
        36%
        4.5
        VE19270_contigs
        151.4Kbp
        2.6Mbp
        VE19271
        1.5%
        18.9
        36.5%
        98.0%
        5.5%
        Enterococcus cecorum
        336.0
        2505
        VE19271_1
        52.2%
        36%
        9.7
        VE19271_2
        47.4%
        37%
        9.7
        VE19271_contigs
        162.8Kbp
        2.6Mbp
        VE19272
        1.7%
        23.1
        36.6%
        98.3%
        4.9%
        Enterococcus cecorum
        96.0
        2172
        VE19272_1
        60.4%
        36%
        11.8
        VE19272_2
        53.8%
        37%
        11.8
        VE19272_contigs
        93.4Kbp
        2.3Mbp
        VE19273
        1.2%
        14.0
        36.6%
        98.4%
        4.0%
        Enterococcus cecorum
        82.0
        2173
        VE19273_1
        49.0%
        36%
        7.1
        VE19273_2
        43.7%
        36%
        7.1
        VE19273_contigs
        98.0Kbp
        2.3Mbp
        VE19274
        5.1%
        15.8
        36.0%
        99.2%
        4.8%
        Enterococcus cecorum
        308.0
        2453
        VE19274_1
        51.3%
        36%
        8.0
        VE19274_2
        49.9%
        36%
        8.0
        VE19274_contigs
        131.7Kbp
        2.6Mbp
        VE19275
        4.1%
        14.4
        36.8%
        99.2%
        2.6%
        Enterococcus cecorum
        1874.0
        2477
        VE19275_1
        50.3%
        36%
        7.3
        VE19275_2
        47.7%
        36%
        7.3
        VE19275_contigs
        61.4Kbp
        3.1Mbp
        VE19276
        1.6%
        20.4
        36.3%
        98.1%
        5.1%
        Enterococcus cecorum
        158.0
        2469
        VE19276_1
        55.4%
        36%
        10.4
        VE19276_2
        48.5%
        36%
        10.4
        VE19276_contigs
        95.7Kbp
        2.6Mbp
        VE19277
        1.4%
        16.3
        36.4%
        98.4%
        4.9%
        Enterococcus cecorum
        327.0
        2415
        VE19277_1
        49.8%
        36%
        8.3
        VE19277_2
        46.2%
        36%
        8.3
        VE19277_contigs
        123.4Kbp
        2.6Mbp
        VE19278
        2.7%
        10.4
        36.7%
        98.6%
        4.5%
        Enterococcus cecorum
        177.0
        2133
        VE19278_1
        45.3%
        36%
        5.3
        VE19278_2
        42.7%
        37%
        5.3
        VE19278_contigs
        47.9Kbp
        2.3Mbp
        VE19279
        2.6%
        13.9
        36.8%
        98.8%
        3.9%
        Enterococcus cecorum
        98.0
        2410
        VE19279_1
        48.7%
        37%
        7.0
        VE19279_2
        45.8%
        37%
        7.0
        VE19279_contigs
        163.0Kbp
        2.5Mbp
        VE19280
        2.3%
        10.1
        36.7%
        98.6%
        3.4%
        Enterococcus cecorum
        171.0
        2373
        VE19280_1
        42.6%
        36%
        5.1
        VE19280_2
        39.4%
        37%
        5.1
        VE19280_contigs
        52.0Kbp
        2.5Mbp
        VE19281
        4.4%
        8.7
        36.7%
        99.0%
        4.3%
        Enterococcus cecorum
        37.0
        2116
        VE19281_1
        42.3%
        36%
        4.4
        VE19281_2
        39.6%
        37%
        4.4
        VE19281_contigs
        143.4Kbp
        2.2Mbp
        VE19282
        2.2%
        11.1
        36.6%
        98.8%
        4.0%
        Enterococcus cecorum
        194.0
        2248
        VE19282_1
        45.1%
        36%
        5.6
        VE19282_2
        43.0%
        36%
        5.6
        VE19282_contigs
        38.4Kbp
        2.4Mbp
        VE19283
        2.0%
        11.6
        36.7%
        98.4%
        4.8%
        Enterococcus cecorum
        162.0
        2404
        VE19283_1
        44.5%
        37%
        5.9
        VE19283_2
        40.4%
        37%
        5.9
        VE19283_contigs
        53.9Kbp
        2.5Mbp
        VE19286
        3.8%
        8.1
        36.3%
        99.0%
        2.4%
        Enterococcus cecorum
        174.0
        2371
        VE19286_1
        39.5%
        36%
        4.1
        VE19286_2
        38.1%
        36%
        4.1
        VE19286_contigs
        122.0Kbp
        2.5Mbp
        VE19287
        4.4%
        14.4
        35.6%
        99.2%
        6.8%
        Enterococcus cecorum
        358.0
        2348
        VE19287_1
        47.2%
        35%
        7.3
        VE19287_2
        44.5%
        36%
        7.3
        VE19287_contigs
        116.8Kbp
        2.5Mbp
        VE19288
        2.8%
        15.7
        36.6%
        98.7%
        4.7%
        Enterococcus cecorum
        112.0
        2417
        VE19288_1
        52.1%
        36%
        7.9
        VE19288_2
        49.4%
        36%
        7.9
        VE19288_contigs
        113.1Kbp
        2.5Mbp
        VE19289
        2.5%
        10.4
        36.3%
        98.5%
        3.8%
        Enterococcus cecorum
        112.0
        2461
        VE19289_1
        43.8%
        36%
        5.3
        VE19289_2
        41.4%
        36%
        5.3
        VE19289_contigs
        116.2Kbp
        2.5Mbp
        VE19291
        2.4%
        10.2
        36.6%
        98.6%
        3.5%
        Enterococcus cecorum
        80.0
        2217
        VE19291_1
        45.1%
        36%
        5.1
        VE19291_2
        41.2%
        36%
        5.1
        VE19291_contigs
        148.0Kbp
        2.3Mbp
        VE19292
        2.6%
        14.7
        36.4%
        98.6%
        3.6%
        Enterococcus cecorum
        131.0
        2405
        VE19292_1
        49.9%
        36%
        7.5
        VE19292_2
        47.0%
        36%
        7.5
        VE19292_contigs
        126.8Kbp
        2.5Mbp
        VE19293
        2.4%
        14.6
        36.4%
        98.6%
        4.1%
        Enterococcus cecorum
        169.0
        2389
        VE19293_1
        50.5%
        36%
        7.4
        VE19293_2
        46.8%
        36%
        7.4
        VE19293_contigs
        89.5Kbp
        2.5Mbp
        VE19294
        4.9%
        15.2
        36.8%
        99.1%
        2.8%
        Enterococcus cecorum
        1628.0
        2188
        VE19294_1
        53.9%
        36%
        7.7
        VE19294_2
        51.6%
        36%
        7.7
        VE19294_contigs
        35.6Kbp
        2.7Mbp
        VE19295
        2.6%
        11.1
        36.8%
        98.8%
        4.0%
        Enterococcus cecorum
        100.0
        2412
        VE19295_1
        43.2%
        37%
        5.6
        VE19295_2
        40.8%
        37%
        5.6
        VE19295_contigs
        163.0Kbp
        2.5Mbp
        VE19296
        4.0%
        9.1
        36.1%
        98.9%
        3.2%
        Enterococcus cecorum
        65.0
        2294
        VE19296_1
        41.3%
        36%
        4.6
        VE19296_2
        39.7%
        36%
        4.6
        VE19296_contigs
        128.6Kbp
        2.4Mbp
        VE19297
        2.5%
        12.5
        36.8%
        98.7%
        3.0%
        Enterococcus cecorum
        78.0
        2202
        VE19297_1
        48.0%
        36%
        6.3
        VE19297_2
        45.4%
        37%
        6.3
        VE19297_contigs
        123.8Kbp
        2.3Mbp
        VE19298
        2.5%
        13.2
        36.5%
        98.8%
        3.9%
        Enterococcus cecorum
        180.0
        2707
        VE19298_1
        47.8%
        36%
        6.7
        VE19298_2
        45.6%
        36%
        6.7
        VE19298_contigs
        98.7Kbp
        2.7Mbp
        VE19299
        2.3%
        12.4
        36.9%
        98.6%
        3.9%
        Enterococcus cecorum
        169.0
        2212
        VE19299_1
        48.2%
        37%
        6.3
        VE19299_2
        45.3%
        37%
        6.3
        VE19299_contigs
        53.8Kbp
        2.3Mbp

        FastQC

        Version: 0.12.1

        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 by sample

        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 overrepresented.

        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 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.

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

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 1/1 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GATCGGAAGAGCACACGTCTGAACTCCAGTCACTACGGAAGTAATCTCGT
        1
        10118
        0.0012%

        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

        Version: 0.23.2

        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.

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        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 59/59 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
        1830.46
        69.18
        81.0%
        VE19205_contigs
        173.8Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        71.0
        3354.32
        120.33
        68.9%
        VE19212_contigs
        197.4Kbp
        0.0K
        635.7Kbp
        2.2Mbp
        72.0
        1856.86
        68.15
        79.6%
        VE19215_contigs
        169.9Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        71.0
        3356.06
        121.03
        68.7%
        VE19223_contigs
        253.6Kbp
        0.0K
        341.1Kbp
        2.1Mbp
        78.0
        1907.93
        63.42
        75.9%
        VE19226_contigs
        174.4Kbp
        0.0K
        498.8Kbp
        2.4Mbp
        64.0
        3342.99
        119.11
        68.7%
        VE19243_contigs
        252.4Kbp
        0.0K
        436.8Kbp
        2.2Mbp
        65.0
        1321.99
        49.82
        81.4%
        VE19244_contigs
        120.0Kbp
        0.0K
        425.2Kbp
        2.3Mbp
        59.0
        1248.18
        50.15
        83.4%
        VE19245_contigs
        161.5Kbp
        0.0K
        355.1Kbp
        2.4Mbp
        47.0
        1176.68
        42.35
        85.4%
        VE19246_contigs
        110.0Kbp
        0.0K
        191.4Kbp
        2.2Mbp
        59.0
        1188.90
        43.06
        82.9%
        VE19247_contigs
        140.0Kbp
        0.0K
        425.7Kbp
        2.3Mbp
        59.0
        1247.45
        49.99
        83.4%
        VE19248_contigs
        137.9Kbp
        0.0K
        275.7Kbp
        2.3Mbp
        55.0
        1217.51
        47.61
        84.0%
        VE19249_contigs
        96.0Kbp
        0.0K
        266.7Kbp
        2.2Mbp
        63.0
        1328.06
        53.38
        82.4%
        VE19250_contigs
        119.2Kbp
        0.0K
        280.5Kbp
        2.3Mbp
        57.0
        1330.39
        49.10
        80.6%
        VE19251_contigs
        45.4Kbp
        0.0K
        124.7Kbp
        2.4Mbp
        80.0
        1912.58
        71.18
        75.8%
        VE19252_contigs
        48.8Kbp
        0.0K
        129.4Kbp
        2.3Mbp
        87.0
        2042.99
        76.16
        76.1%
        VE19253_contigs
        210.5Kbp
        0.0K
        437.5Kbp
        2.2Mbp
        65.0
        1324.49
        49.71
        81.4%
        VE19255_contigs
        143.4Kbp
        0.0K
        355.0Kbp
        2.8Mbp
        56.0
        1035.93
        42.04
        85.4%
        VE19256_contigs
        80.0Kbp
        0.0K
        187.5Kbp
        2.5Mbp
        56.0
        1227.54
        45.68
        84.6%
        VE19257_contigs
        137.4Kbp
        0.0K
        557.0Kbp
        2.6Mbp
        54.0
        1020.27
        42.40
        85.3%
        VE19258_contigs
        133.2Kbp
        0.0K
        361.5Kbp
        2.6Mbp
        53.0
        1037.80
        43.40
        85.6%
        VE19259_contigs
        137.4Kbp
        0.0K
        556.8Kbp
        2.6Mbp
        53.0
        1020.81
        42.45
        85.5%
        VE19260_contigs
        94.6Kbp
        0.0K
        536.1Kbp
        2.5Mbp
        46.0
        1034.19
        41.32
        85.3%
        VE19261_contigs
        110.9Kbp
        0.0K
        205.4Kbp
        2.4Mbp
        57.0
        1214.08
        45.48
        84.3%
        VE19262_contigs
        98.7Kbp
        0.0K
        227.2Kbp
        2.5Mbp
        66.0
        1219.74
        46.08
        85.2%
        VE19263_contigs
        116.2Kbp
        0.0K
        367.3Kbp
        2.5Mbp
        51.0
        1009.58
        40.32
        84.9%
        VE19264_contigs
        140.7Kbp
        0.0K
        379.2Kbp
        2.3Mbp
        67.0
        1206.82
        45.88
        82.7%
        VE19265_contigs
        135.7Kbp
        0.0K
        322.4Kbp
        2.4Mbp
        59.0
        1228.84
        46.37
        84.6%
        VE19266_contigs
        187.3Kbp
        0.0K
        300.0Kbp
        2.5Mbp
        56.0
        1205.02
        44.04
        84.6%
        VE19267_contigs
        44.7Kbp
        0.0K
        176.5Kbp
        2.6Mbp
        73.0
        2025.00
        76.62
        77.1%
        VE19268_contigs
        53.8Kbp
        0.0K
        134.6Kbp
        2.3Mbp
        82.0
        2036.89
        75.15
        76.1%
        VE19269_contigs
        126.8Kbp
        0.0K
        280.5Kbp
        2.4Mbp
        52.0
        1203.40
        43.44
        84.3%
        VE19270_contigs
        151.4Kbp
        0.0K
        458.5Kbp
        2.6Mbp
        60.0
        1210.83
        45.35
        84.6%
        VE19271_contigs
        162.8Kbp
        0.0K
        458.3Kbp
        2.6Mbp
        62.0
        1210.87
        46.13
        84.6%
        VE19272_contigs
        93.4Kbp
        0.0K
        266.3Kbp
        2.3Mbp
        62.0
        1327.04
        53.39
        82.2%
        VE19273_contigs
        98.0Kbp
        0.0K
        266.7Kbp
        2.3Mbp
        61.0
        1323.96
        53.40
        82.4%
        VE19274_contigs
        131.7Kbp
        0.0K
        301.7Kbp
        2.6Mbp
        54.0
        1214.95
        44.42
        84.8%
        VE19275_contigs
        61.4Kbp
        0.0K
        263.2Kbp
        3.1Mbp
        49.0
        1006.11
        39.61
        84.6%
        VE19276_contigs
        95.7Kbp
        0.0K
        334.3Kbp
        2.6Mbp
        56.0
        1007.33
        40.66
        84.9%
        VE19277_contigs
        123.4Kbp
        0.0K
        327.6Kbp
        2.6Mbp
        51.0
        1205.66
        43.28
        84.4%
        VE19278_contigs
        47.9Kbp
        0.0K
        151.1Kbp
        2.3Mbp
        88.0
        1986.21
        72.33
        74.5%
        VE19279_contigs
        163.0Kbp
        0.0K
        300.9Kbp
        2.5Mbp
        54.0
        1197.41
        42.42
        84.2%
        VE19280_contigs
        52.0Kbp
        0.0K
        144.0Kbp
        2.5Mbp
        85.0
        2115.84
        78.73
        74.1%
        VE19281_contigs
        143.4Kbp
        0.0K
        256.0Kbp
        2.2Mbp
        61.0
        1351.41
        49.87
        80.9%
        VE19282_contigs
        38.4Kbp
        0.0K
        120.0Kbp
        2.4Mbp
        78.0
        1995.84
        72.33
        75.0%
        VE19283_contigs
        53.9Kbp
        0.0K
        144.5Kbp
        2.5Mbp
        90.0
        2045.99
        77.44
        75.7%
        VE19286_contigs
        122.0Kbp
        0.0K
        255.4Kbp
        2.5Mbp
        55.0
        1213.97
        45.18
        84.2%
        VE19287_contigs
        116.8Kbp
        0.0K
        305.6Kbp
        2.5Mbp
        58.0
        1234.23
        46.40
        84.2%
        VE19288_contigs
        113.1Kbp
        0.0K
        280.5Kbp
        2.5Mbp
        58.0
        1232.68
        46.11
        84.5%
        VE19289_contigs
        116.2Kbp
        0.0K
        539.3Kbp
        2.5Mbp
        51.0
        1007.23
        40.20
        84.9%
        VE19291_contigs
        148.0Kbp
        0.0K
        311.5Kbp
        2.3Mbp
        63.0
        1205.22
        45.36
        82.5%
        VE19292_contigs
        126.8Kbp
        0.0K
        327.7Kbp
        2.5Mbp
        48.0
        1207.08
        43.65
        84.1%
        VE19293_contigs
        89.5Kbp
        0.0K
        183.6Kbp
        2.5Mbp
        57.0
        1134.45
        42.13
        83.7%
        VE19294_contigs
        35.6Kbp
        0.0K
        151.1Kbp
        2.7Mbp
        88.0
        1976.71
        71.34
        74.5%
        VE19295_contigs
        163.0Kbp
        0.0K
        375.9Kbp
        2.5Mbp
        56.0
        1198.42
        42.69
        84.3%
        VE19296_contigs
        128.6Kbp
        0.0K
        280.5Kbp
        2.4Mbp
        55.0
        1230.79
        46.70
        84.2%
        VE19297_contigs
        123.8Kbp
        0.0K
        250.9Kbp
        2.3Mbp
        60.0
        1207.22
        45.39
        82.1%
        VE19298_contigs
        98.7Kbp
        0.0K
        190.8Kbp
        2.7Mbp
        61.0
        1391.97
        52.88
        82.5%
        VE19299_contigs
        53.8Kbp
        0.0K
        134.2Kbp
        2.3Mbp
        89.0
        2033.52
        74.91
        76.1%

        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.

        loading..

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1
        fastp0.23.2

        MultiQC v1.19 - Written by Phil Ewels, available on GitHub.

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