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

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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 1.0.dev0

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

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

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

        MultiQC is published in Bioinformatics:

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

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

        Report generated on 2019-12-23, 18:12 based on data in: /beegfs/mk5636/logs/html/H2CVWAFX2/merged

        General Statistics

        Showing 17/17 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        H2CVWAFX2_n01_AH10456-3h-Red1
        35.7%
        41%
        9.4
        H2CVWAFX2_n01_AH10456-3h-input
        28.7%
        40%
        10.2
        H2CVWAFX2_n01_AH7797-3h-34C-Top2-spike
        34.5%
        42%
        9.6
        H2CVWAFX2_n01_AH7797-3h-34C-Top2-spikerep
        32.2%
        41%
        8.4
        H2CVWAFX2_n01_AH7797-3h-34C-input-spike
        27.1%
        39%
        9.4
        H2CVWAFX2_n01_AH7797-3h-34C-input-spikerep
        31.4%
        39%
        12.7
        H2CVWAFX2_n01_AH7797-3h-Nop1
        33.1%
        41%
        11.1
        H2CVWAFX2_n01_AH7797-3h-inputNop1
        30.8%
        41%
        10.1
        H2CVWAFX2_n01_AH7797-4h-Top2
        40.0%
        42%
        11.6
        H2CVWAFX2_n01_AH7797-4h-inputTop2
        31.6%
        40%
        11.7
        H2CVWAFX2_n01_AH7838-3h-Red1
        40.2%
        41%
        12.0
        H2CVWAFX2_n01_AH7838-3h-input
        32.9%
        40%
        12.7
        H2CVWAFX2_n01_AH8632-3h-Top2
        35.7%
        41%
        11.7
        H2CVWAFX2_n01_AH8632-3h-input
        32.1%
        40%
        12.1
        H2CVWAFX2_n01_AH9003-3h-Red1
        35.7%
        39%
        11.1
        H2CVWAFX2_n01_AH9003-3h-input
        32.6%
        39%
        11.6
        H2CVWAFX2_n01_undetermined
        47.9%
        42%
        11.4

        Demultiplexing Report

        Demultiplexing Report
        Total Read Count: Total number of PF (Passing Filter) reads in this library.
        Portion: The proportion of reads that represent the individual library in the entire Library Pool.

        Showing 17/17 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        11,420,739
        6.1
        AH8632-3h-input
        12,075,904
        6.5
        AH9003-3h-input
        11,587,401
        6.2
        AH7797-3h-inputNop1
        10,140,521
        5.4
        AH7797-4h-inputTop2
        11,707,040
        6.3
        AH7797-3h-34C-input-spike
        9,414,615
        5.0
        AH7797-3h-34C-input-spikerep
        12,740,460
        6.8
        AH7838-3h-input
        12,658,168
        6.8
        AH10456-3h-input
        10,231,476
        5.5
        AH8632-3h-Top2
        11,692,920
        6.3
        AH9003-3h-Red1
        11,113,375
        5.9
        AH7797-3h-Nop1
        11,122,362
        6.0
        AH7797-4h-Top2
        11,580,861
        6.2
        AH7797-3h-34C-Top2-spike
        9,585,422
        5.1
        AH7797-3h-34C-Top2-spikerep
        8,386,841
        4.5
        AH7838-3h-Red1
        11,976,120
        6.4
        AH10456-3h-Red1
        9,438,353
        5.1

        Barcodes of Undetermined Reads

        Barcodes of Undetermined Reads
        We have determined the barcodes of your undetermined reads (reads containing a barcode that you did not encode in your metadata). Here are the top 20 barcodes belonging to the undetermined reads. The full list is available here.

        Showing 20/20 rows and 2/2 columns.
        Sample NameCountFrequency (%)
        GGGGGG
        7486249.0
        65.5
        NNNNNN
        241324.0
        2.1
        GGGGGC
        55090.0
        0.5
        GGCGGG
        46505.0
        0.4
        GTGGGG
        42358.0
        0.4
        GCGGGG
        41283.0
        0.4
        GGGGGT
        39823.0
        0.3
        CGGGGG
        37718.0
        0.3
        GGGGCG
        33675.0
        0.3
        CCCGTC
        32732.0
        0.3
        GGGGTG
        30960.0
        0.3
        GGGCGG
        30953.0
        0.3
        CAGAAA
        28891.0
        0.2
        GGGTGG
        28781.0
        0.2
        GGTGGG
        28366.0
        0.2
        CAGTCA
        26572.0
        0.2
        GACAAA
        25286.0
        0.2
        ATTAAA
        23898.0
        0.2
        GTCCCG
        22350.0
        0.2
        TGGGGG
        22237.0
        0.2

        Run Statistics

        Run Statistics

        Showing 1/1 rows and 4/4 columns.
        Sample NameTotal # of Single-End ReadsTotal # PF Reads% Undetermined % PhiX Aligned
        4.0
        215,487,756
        186,872,578
        6.1
        1.9

        FastQC

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

        Sequence Quality Histograms

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

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        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

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        Per Base Sequence Content

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

        Click a heatmap 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. See the FastQC help.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.

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        Sequence Length Distribution

        All samples have sequences of a single length (101bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

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        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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        MultiQC v1.0.dev0 - Written by Phil Ewels, available on GitHub.

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