..plots loading..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

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

        Choose Plots

        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

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        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, 03:05 based on data in: /beegfs/mk5636/logs/html/CCY3TACXX/4

        General Statistics

        Showing 20/20 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        CCY3TACXX_l04_n01_D3S1
        69.6%
        53%
        25.0
        CCY3TACXX_l04_n01_D3S2
        69.5%
        52%
        27.3
        CCY3TACXX_l04_n01_D3S3
        69.7%
        52%
        30.4
        CCY3TACXX_l04_n01_D3S4
        65.8%
        52%
        22.2
        CCY3TACXX_l04_n01_D3S5
        69.6%
        53%
        25.7
        CCY3TACXX_l04_n01_D3S6
        62.0%
        52%
        15.7
        CCY3TACXX_l04_n01_D3S7
        65.8%
        52%
        25.2
        CCY3TACXX_l04_n01_D3S8
        67.2%
        52%
        25.0
        CCY3TACXX_l04_n01_D3S9
        67.5%
        52%
        20.0
        CCY3TACXX_l04_n01_undetermined
        90.3%
        45%
        18.6
        CCY3TACXX_l04_n02_D3S1
        71.5%
        55%
        25.0
        CCY3TACXX_l04_n02_D3S2
        71.0%
        55%
        27.3
        CCY3TACXX_l04_n02_D3S3
        71.1%
        55%
        30.4
        CCY3TACXX_l04_n02_D3S4
        67.7%
        55%
        22.2
        CCY3TACXX_l04_n02_D3S5
        70.6%
        55%
        25.7
        CCY3TACXX_l04_n02_D3S6
        62.7%
        54%
        15.7
        CCY3TACXX_l04_n02_D3S7
        66.9%
        54%
        25.2
        CCY3TACXX_l04_n02_D3S8
        68.3%
        55%
        25.0
        CCY3TACXX_l04_n02_D3S9
        68.9%
        55%
        20.0
        CCY3TACXX_l04_n02_undetermined
        88.8%
        46%
        18.6

        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 (%)
        NNNNNN
        111187.0
        0.6
        TAGGCA
        79758.0
        0.4
        GATGTA
        58905.0
        0.3
        CCCCCC
        55565.0
        0.3
        GAGCAC
        54475.0
        0.3
        GACCAA
        52246.0
        0.3
        GCCCAA
        51481.0
        0.3
        ACTGAA
        49283.0
        0.3
        CAGCAC
        47875.0
        0.3
        CGCCCC
        47857.0
        0.3
        CGCCCA
        46419.0
        0.2
        ATACGA
        46206.0
        0.2
        GAGCAA
        46049.0
        0.2
        CAGCCC
        45626.0
        0.2
        GACCAC
        45553.0
        0.2
        GAGAAG
        45154.0
        0.2
        CGGCCC
        45094.0
        0.2
        CCGCTC
        44803.0
        0.2
        GGCCAT
        41692.0
        0.2
        CACCCC
        41496.0
        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
        4.0
        246,693,552
        235,013,285
        7.9
        8.2

        Lane 4 Demultiplexing Report

        Lane 4 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
        18,552,748
        7.9
        D3S1
        24,965,362
        10.6
        D3S2
        27,298,786
        11.6
        D3S3
        30,444,076
        13.0
        D3S4
        22,204,932
        9.4
        D3S5
        25,661,862
        10.9
        D3S6
        15,729,322
        6.7
        D3S7
        25,184,095
        10.7
        D3S8
        24,983,049
        10.6
        D3S9
        19,989,053
        8.5

        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.

        loading..

        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.

        loading..

        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.

        loading..

        Per Base N Content

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

        loading..

        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.

        loading..

        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.