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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 2019-04-26, 00:04 based on data in: /beegfs/mk5636/logs/html/HKLVVAFXY/merged

        General Statistics

        Showing 18/18 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        HKLVVAFXY_n01_3LG_N-2
        3.5%
        45%
        0.5
        HKLVVAFXY_n01_3LG_N-3
        7.1%
        49%
        1.2
        HKLVVAFXY_n01_3LG_N-4
        5.0%
        50%
        1.1
        HKLVVAFXY_n01_3LG_N-5
        6.5%
        50%
        0.9
        HKLVVAFXY_n01_3LG_N-6
        8.4%
        50%
        0.8
        HKLVVAFXY_n01_3LG_N-7
        8.4%
        50%
        1.4
        HKLVVAFXY_n01_3LG_N-8
        6.8%
        49%
        0.5
        HKLVVAFXY_n01_3LG_N-9
        7.5%
        49%
        1.2
        HKLVVAFXY_n01_undetermined
        2.0%
        51%
        9.6
        HKLVVAFXY_n02_3LG_N-2
        0.2%
        44%
        0.5
        HKLVVAFXY_n02_3LG_N-3
        0.2%
        51%
        1.2
        HKLVVAFXY_n02_3LG_N-4
        0.1%
        52%
        1.1
        HKLVVAFXY_n02_3LG_N-5
        0.1%
        48%
        0.9
        HKLVVAFXY_n02_3LG_N-6
        0.2%
        49%
        0.8
        HKLVVAFXY_n02_3LG_N-7
        0.2%
        51%
        1.4
        HKLVVAFXY_n02_3LG_N-8
        0.2%
        48%
        0.5
        HKLVVAFXY_n02_3LG_N-9
        0.3%
        48%
        1.2
        HKLVVAFXY_n02_undetermined
        0.2%
        53%
        9.6

        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 9/9 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        9,642,939
        56.7
        3LG_N-2
        452,894
        2.6
        3LG_N-3
        1,212,273
        7.0
        3LG_N-4
        1,104,103
        6.4
        3LG_N-5
        862,380
        5.0
        3LG_N-6
        799,772
        4.6
        3LG_N-7
        1,356,542
        7.8
        3LG_N-8
        498,687
        2.9
        3LG_N-9
        1,208,561
        7.0

        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
        659882.0
        6.8
        GGGGGG
        162306.0
        1.7
        TTACCC
        73862.0
        0.8
        TGCCCC
        67620.0
        0.7
        CCTTGT
        61784.0
        0.6
        TTCCCG
        59619.0
        0.6
        CCATTT
        52629.0
        0.6
        GGCCCT
        51340.0
        0.5
        TTCCCC
        51032.0
        0.5
        CCGTGA
        47523.0
        0.5
        CGAGGG
        47413.0
        0.5
        CCGGTG
        46667.0
        0.5
        ACTGGC
        46220.0
        0.5
        CGGTGG
        44991.0
        0.5
        CGTTGA
        42407.0
        0.4
        GGCACT
        41907.0
        0.4
        CCCGTG
        39315.0
        0.4
        GGCCCA
        38860.0
        0.4
        AATTGC
        38428.0
        0.4
        AGATGA
        38259.0
        0.4

        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
        248,289,684
        17,138,151
        56.7
        0.0

        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.

        18 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.