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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 2019-05-13, 06:05 based on data in: /beegfs/mk5636/logs/html/CCY3TACXX/8

        General Statistics

        Showing 20/20 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        CCY3TACXX_l08_n01_S3S1
        69.6%
        52%
        28.7
        CCY3TACXX_l08_n01_S3S2
        72.4%
        52%
        45.3
        CCY3TACXX_l08_n01_S3S3
        68.6%
        52%
        35.5
        CCY3TACXX_l08_n01_S3S4
        62.4%
        51%
        31.6
        CCY3TACXX_l08_n01_S3S5
        69.3%
        52%
        37.8
        CCY3TACXX_l08_n01_S3S6
        59.8%
        50%
        29.5
        CCY3TACXX_l08_n01_S3S7
        64.2%
        51%
        25.4
        CCY3TACXX_l08_n01_S3S8
        66.2%
        52%
        29.5
        CCY3TACXX_l08_n01_S3S9
        90.0%
        44%
        0.3
        CCY3TACXX_l08_n01_undetermined
        87.2%
        46%
        17.8
        CCY3TACXX_l08_n02_S3S1
        67.6%
        54%
        28.7
        CCY3TACXX_l08_n02_S3S2
        71.8%
        55%
        45.3
        CCY3TACXX_l08_n02_S3S3
        67.7%
        54%
        35.5
        CCY3TACXX_l08_n02_S3S4
        63.5%
        53%
        31.6
        CCY3TACXX_l08_n02_S3S5
        68.1%
        55%
        37.8
        CCY3TACXX_l08_n02_S3S6
        58.5%
        52%
        29.5
        CCY3TACXX_l08_n02_S3S7
        62.9%
        54%
        25.4
        CCY3TACXX_l08_n02_S3S8
        64.7%
        54%
        29.5
        CCY3TACXX_l08_n02_S3S9
        88.9%
        44%
        0.3
        CCY3TACXX_l08_n02_undetermined
        85.0%
        46%
        17.8

        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 10/10 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        17,766,566
        6.3
        S3S1
        28,665,230
        10.2
        S3S2
        45,341,597
        16.1
        S3S3
        35,492,111
        12.6
        S3S4
        31,641,189
        11.2
        S3S5
        37,829,995
        13.4
        S3S6
        29,521,055
        10.5
        S3S7
        25,383,050
        9.0
        S3S8
        29,523,875
        10.5
        S3S9
        284,647
        0.1

        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 (%)
        CCTATC
        144982.0
        0.8
        NNNNNN
        133812.0
        0.8
        GAGCAC
        117631.0
        0.7
        GATGTA
        92690.0
        0.5
        GAGCAA
        87443.0
        0.5
        TAGGCA
        86359.0
        0.5
        GACCAA
        81519.0
        0.5
        CAGCAC
        77637.0
        0.4
        GACCAC
        73505.0
        0.4
        CAGCCC
        69739.0
        0.4
        GAGAAC
        69165.0
        0.4
        GCCCAA
        67336.0
        0.4
        GAGAAG
        65586.0
        0.4
        GACAAC
        65116.0
        0.4
        GAGCCC
        60279.0
        0.3
        GAGGAC
        58198.0
        0.3
        GAGGAG
        57571.0
        0.3
        GACCCC
        57207.0
        0.3
        ACTGAA
        56162.0
        0.3
        CACCCC
        54376.0
        0.3

        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
        303,320,128
        281,449,315
        6.3
        6.4

        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 (51bp).

        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.

        20 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.

        No samples found with any adapter contamination > 0.1%

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

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