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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 2019-10-11, 17:10 based on data in: /beegfs/mk5636/logs/html/HTHTVAFXY/merged

        General Statistics

        Showing 18/18 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        HTHTVAFXY_n01_AtChl1.5
        0.2%
        49%
        21
        0.0
        HTHTVAFXY_n01_AtNLP7
        0.1%
        50%
        21
        0.0
        HTHTVAFXY_n01_At_Chl1.5
        18.3%
        50%
        21
        19.1
        HTHTVAFXY_n01_At_NLP7
        36.6%
        50%
        21
        24.0
        HTHTVAFXY_n01_Col-1
        0.0%
        49%
        21
        0.0
        HTHTVAFXY_n01_Col-2
        1.0%
        46%
        21
        0.0
        HTHTVAFXY_n01_Columbia-1
        25.1%
        49%
        21
        28.1
        HTHTVAFXY_n01_Columbia-2
        18.6%
        45%
        21
        38.4
        HTHTVAFXY_n01_undetermined
        68.7%
        46%
        21
        11.6
        HTHTVAFXY_n02_AtChl1.5
        0.2%
        41%
        129
        0.0
        HTHTVAFXY_n02_AtNLP7
        1.8%
        41%
        129
        0.0
        HTHTVAFXY_n02_At_Chl1.5
        58.1%
        39%
        129
        19.1
        HTHTVAFXY_n02_At_NLP7
        58.5%
        37%
        129
        24.0
        HTHTVAFXY_n02_Col-1
        0.0%
        41%
        129
        0.0
        HTHTVAFXY_n02_Col-2
        0.2%
        43%
        129
        0.0
        HTHTVAFXY_n02_Columbia-1
        64.7%
        39%
        129
        28.1
        HTHTVAFXY_n02_Columbia-2
        59.3%
        43%
        129
        38.4
        HTHTVAFXY_n02_undetermined
        59.1%
        45%
        129
        11.6

        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 5/5 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        11,630,046
        9.6
        Columbia-1
        28,077,370
        23.2
        Columbia-2
        38,401,866
        31.7
        At_NLP7
        23,963,394
        19.8
        At_Chl1.5
        19,070,044
        15.7

        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 (%)
        GGGGGGGG
        8660964.0
        74.5
        GTACTAGA
        90035.0
        0.8
        CGTATAGA
        79066.0
        0.7
        CTACTAGA
        76186.0
        0.7
        NNNNNNNN
        73589.0
        0.6
        CGTACAGA
        65271.0
        0.6
        GGTGGGGG
        58806.0
        0.5
        ACAACAAC
        56192.0
        0.5
        AAAACAAA
        51387.0
        0.4
        AGTAATAA
        49257.0
        0.4
        TAGGCGAA
        44215.0
        0.4
        CGACTAGA
        44208.0
        0.4
        CGTCTAGA
        43190.0
        0.4
        CGGGGGGG
        41900.0
        0.4
        CGGCCGAG
        40765.0
        0.3
        TCTGAGCA
        39638.0
        0.3
        GGGGGCGG
        32729.0
        0.3
        AAACCCAA
        31779.0
        0.3
        TAAGCGAA
        31609.0
        0.3
        CCAACAAC
        29958.0
        0.3

        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
        192,733,160
        121,142,720
        9.6
        nan

        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 (129bp , 21bp). See the General Statistics Table.

        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.