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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 2019-01-18, 23:01 based on data in: /beegfs/mk5636/logs/html/HGGLTBGX9/merged

        General Statistics

        Showing 17/17 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        HGGLTBGX9_n01_10_CRF4_BIO_180_R1
        88.6%
        44%
        18.5
        HGGLTBGX9_n01_11_RAV1_BIO_180_R1
        78.2%
        46%
        16.3
        HGGLTBGX9_n01_12_BZIP3_BIO_10_R2
        55.8%
        44%
        99.7
        HGGLTBGX9_n01_13_CRF4_BIO_10_R2
        47.7%
        44%
        33.7
        HGGLTBGX9_n01_14_BZIP3_BIO_180_R2
        49.5%
        43%
        22.2
        HGGLTBGX9_n01_15_INPUT_BZIP3_5_R1
        76.4%
        45%
        15.9
        HGGLTBGX9_n01_16_INPUT_CRF4_5_R1
        85.7%
        47%
        15.5
        HGGLTBGX9_n01_1_NLP7_BIO_1_R1
        75.9%
        45%
        14.4
        HGGLTBGX9_n01_2_NLP7_BIO_3_R1
        90.0%
        46%
        15.9
        HGGLTBGX9_n01_3_BZIP3_BIO_5_R1
        92.8%
        47%
        6.9
        HGGLTBGX9_n01_4_CRF4_BIO_5_R1
        91.4%
        46%
        13.7
        HGGLTBGX9_n01_5_RAV1_BIO_5_R1
        80.0%
        46%
        14.0
        HGGLTBGX9_n01_6_BZIP3_BIO_10_R1
        74.8%
        43%
        17.2
        HGGLTBGX9_n01_7_CRF4_BIO_10_R1
        89.8%
        47%
        13.3
        HGGLTBGX9_n01_8_RAV1_BIO_10_R1
        90.3%
        47%
        9.9
        HGGLTBGX9_n01_9_BZIP3_BIO_180_R1
        74.7%
        45%
        16.5
        HGGLTBGX9_n01_undetermined
        83.3%
        44%
        23.3

        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
        23,349,481
        6.4
        16_INPUT_CRF4_5_R1
        15,483,102
        4.2
        15_INPUT_BZIP3_5_R1
        15,932,519
        4.3
        14_BZIP3_BIO_180_R2
        22,217,338
        6.1
        13_CRF4_BIO_10_R2
        33,672,716
        9.2
        12_BZIP3_BIO_10_R2
        99,741,184
        27.2
        11_RAV1_BIO_180_R1
        16,258,209
        4.4
        10_CRF4_BIO_180_R1
        18,505,840
        5.0
        9_BZIP3_BIO_180_R1
        16,507,218
        4.5
        8_RAV1_BIO_10_R1
        9,929,298
        2.7
        7_CRF4_BIO_10_R1
        13,291,784
        3.6
        6_BZIP3_BIO_10_R1
        17,174,150
        4.7
        5_RAV1_BIO_5_R1
        13,954,515
        3.8
        4_CRF4_BIO_5_R1
        13,701,687
        3.7
        3_BZIP3_BIO_5_R1
        6,889,183
        1.9
        2_NLP7_BIO_3_R1
        15,873,774
        4.3
        1_NLP7_BIO_1_R1
        14,424,453
        3.9

        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
        17515871.0
        75.0
        ATACAA
        112770.0
        0.5
        ATAGTA
        103278.0
        0.4
        CTGTAA
        91364.0
        0.4
        CATATA
        73033.0
        0.3
        ATAAAA
        67134.0
        0.3
        CATCAA
        64612.0
        0.3
        AATTTA
        63272.0
        0.3
        ATTTAA
        62281.0
        0.3
        CTATTA
        59557.0
        0.3
        CTATAA
        53951.0
        0.2
        CTTTGT
        48880.0
        0.2
        ACTAAA
        46703.0
        0.2
        ATAACC
        46141.0
        0.2
        CCTTGT
        45510.0
        0.2
        AGAAAA
        44961.0
        0.2
        AATAAA
        43712.0
        0.2
        CATCTA
        42692.0
        0.2
        GGGGGT
        41359.0
        0.2
        AGAACA
        40849.0
        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
        396,249,472
        366,906,451
        6.4
        4.6

        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 (76bp).

        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.