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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 2019-12-17, 05:12 based on data in: /beegfs/mk5636/logs/html/CCY3RACXX/8

        General Statistics

        Showing 24/24 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        CCY3RACXX_l08_n01_FounderF.A1.a
        1.2%
        49%
        11.7
        CCY3RACXX_l08_n01_FounderF.A1.b
        0.9%
        49%
        15.8
        CCY3RACXX_l08_n01_FounderF.B1.a
        1.2%
        49%
        12.7
        CCY3RACXX_l08_n01_FounderF.B1.b
        1.1%
        49%
        11.4
        CCY3RACXX_l08_n01_FounderMale.1
        0.2%
        45%
        13.3
        CCY3RACXX_l08_n01_QG2987.fGM
        0.2%
        46%
        13.6
        CCY3RACXX_l08_n01_QG2987.mGF
        0.2%
        45%
        17.5
        CCY3RACXX_l08_n01_QG2990.1fGM
        1.0%
        46%
        17.6
        CCY3RACXX_l08_n01_QG2990.1mGF
        0.2%
        45%
        14.6
        CCY3RACXX_l08_n01_QG2990.2fGM
        1.2%
        50%
        18.0
        CCY3RACXX_l08_n01_QG2990.2mGF
        0.4%
        45%
        16.5
        CCY3RACXX_l08_n01_undetermined
        61.7%
        45%
        14.1
        CCY3RACXX_l08_n02_FounderF.A1.a
        31.8%
        49%
        11.7
        CCY3RACXX_l08_n02_FounderF.A1.b
        33.5%
        49%
        15.8
        CCY3RACXX_l08_n02_FounderF.B1.a
        34.5%
        49%
        12.7
        CCY3RACXX_l08_n02_FounderF.B1.b
        33.5%
        49%
        11.4
        CCY3RACXX_l08_n02_FounderMale.1
        11.2%
        45%
        13.3
        CCY3RACXX_l08_n02_QG2987.fGM
        10.4%
        46%
        13.6
        CCY3RACXX_l08_n02_QG2987.mGF
        11.9%
        45%
        17.5
        CCY3RACXX_l08_n02_QG2990.1fGM
        12.8%
        46%
        17.6
        CCY3RACXX_l08_n02_QG2990.1mGF
        9.9%
        44%
        14.6
        CCY3RACXX_l08_n02_QG2990.2fGM
        43.2%
        50%
        18.0
        CCY3RACXX_l08_n02_QG2990.2mGF
        18.4%
        45%
        16.5
        CCY3RACXX_l08_n02_undetermined
        80.9%
        45%
        14.1

        Lane 8 Demultiplexing Report

        Lane 8 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 12/12 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        14,092,570
        8.0
        QG2990.1mGF
        14,573,299
        8.2
        QG2990.2mGF
        16,455,921
        9.3
        QG2987.mGF
        17,452,339
        9.9
        QG2990.1fGM
        17,633,222
        10.0
        QG2990.2fGM
        18,034,862
        10.2
        QG2987.fGM
        13,570,648
        7.7
        FounderMale.1
        13,333,740
        7.5
        FounderF.A1.a
        11,743,953
        6.6
        FounderF.B1.a
        12,698,409
        7.2
        FounderF.A1.b
        15,833,733
        9.0
        FounderF.B1.b
        11,393,874
        6.4

        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 (%)
        CCCCCC
        118246.0
        0.8
        CCCCCA
        61579.0
        0.4
        CCCACC
        56863.0
        0.4
        CTCCCC
        55541.0
        0.4
        AGTGAT
        54440.0
        0.4
        TAGGCA
        54113.0
        0.4
        NNNNNN
        53862.0
        0.4
        CCCCCT
        52015.0
        0.4
        GATGTA
        51380.0
        0.4
        CCTCCC
        50044.0
        0.4
        CCCCAC
        49281.0
        0.3
        CCCTCC
        45260.0
        0.3
        CCCCTC
        44099.0
        0.3
        CACCCC
        44002.0
        0.3
        CGCCCC
        41386.0
        0.3
        ATACGA
        40466.0
        0.3
        GCCCAA
        40030.0
        0.3
        CCCGCC
        38371.0
        0.3
        GCCCCC
        36820.0
        0.3
        TCCCCC
        35031.0
        0.2

        Lane Statistics

        Lane Statistics

        Showing 1/1 rows and 4/4 columns.
        Sample NameTotal # of Single-End ReadsTotal # PF Reads% Undetermined % PhiX Aligned
        8.0
        182,286,192
        176,816,570
        8.0
        3.8

        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.

        24 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. 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.