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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 2018-04-02, 16:04 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HJT2TBGX5/merged

        Welcome! Not sure where to start?   Watch a tutorial video   (6:06)

        General Statistics

        Showing 24/24 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        HJT2TBGX5_n01_2a_t4d9a
        90.4%
        50%
        32.4
        HJT2TBGX5_n01_2a_t4d9b
        90.0%
        46%
        29.4
        HJT2TBGX5_n01_2a_t6d14b
        92.9%
        48%
        40.2
        HJT2TBGX5_n01_2b_c1d9a
        89.5%
        45%
        35.1
        HJT2TBGX5_n01_2b_c1d9b
        91.6%
        51%
        35.3
        HJT2TBGX5_n01_2b_c2d9a
        92.5%
        60%
        37.9
        HJT2TBGX5_n01_2b_c2d9b
        89.3%
        46%
        27.2
        HJT2TBGX5_n01_2b_t1d9a
        91.7%
        51%
        47.9
        HJT2TBGX5_n01_2b_t1d9b
        90.9%
        46%
        39.6
        HJT2TBGX5_n01_2b_t2d9a
        90.2%
        47%
        33.1
        HJT2TBGX5_n01_2b_t3d14a
        90.3%
        46%
        35.7
        HJT2TBGX5_n01_2b_t4d14a
        91.9%
        46%
        54.0
        HJT2TBGX5_n02_2a_t4d9a
        85.0%
        49%
        32.4
        HJT2TBGX5_n02_2a_t4d9b
        82.4%
        45%
        29.4
        HJT2TBGX5_n02_2a_t6d14b
        86.6%
        48%
        40.2
        HJT2TBGX5_n02_2b_c1d9a
        84.8%
        45%
        35.1
        HJT2TBGX5_n02_2b_c1d9b
        85.5%
        50%
        35.3
        HJT2TBGX5_n02_2b_c2d9a
        87.7%
        60%
        37.9
        HJT2TBGX5_n02_2b_c2d9b
        84.4%
        46%
        27.2
        HJT2TBGX5_n02_2b_t1d9a
        83.5%
        50%
        47.9
        HJT2TBGX5_n02_2b_t1d9b
        86.1%
        46%
        39.6
        HJT2TBGX5_n02_2b_t2d9a
        83.1%
        47%
        33.1
        HJT2TBGX5_n02_2b_t3d14a
        83.2%
        46%
        35.7
        HJT2TBGX5_n02_2b_t4d14a
        85.9%
        46%
        54.0

        Run Statistics

        Run Statistics

        Showing 1/1 rows and 4/4 columns.
        Number of LanesTotal # of Single-End ReadsTotal # PF ReadsUndetermined % PhiX Aligned
        4.0
        506246567
        467534675
        4.2
        0.9

        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.
        Perfect: The percentage of reads in this library which have a barcode perfectly matching the barcode specified in TuboWeb. The remainder of reads have mismatches upto the max number of mismatches specified in TuboWeb (Allowed barcode mismatch option in your Library Pool).

        Showing 12/12 rows and 3/3 columns.
        LibraryTotal Read CountPortion (%)Perfect (%)
        2b_t1d9b
        39615246
        8.8
        96.4
        2b_c1d9b
        35320711
        7.9
        96.2
        2b_t2d9a
        33089323
        7.4
        95.4
        2b_t4d14a
        54035892
        12.1
        96.3
        2b_t1d9a
        47856772
        10.7
        96.1
        2a_t6d14b
        40234508
        9.0
        96.2
        2b_c2d9a
        37882372
        8.5
        97.2
        2b_t3d14a
        35737701
        8.0
        95.5
        2a_t4d9b
        29431154
        6.6
        95.5
        2b_c2d9b
        27236660
        6.1
        95.5
        2a_t4d9a
        32390116
        7.2
        95.7
        2b_c1d9a
        35059756
        7.8
        95.4

        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
        24
        0
        0

        The mean quality value across each base position in the read. See the FastQC help.

        Created with Highcharts 5.0.6Position (bp)Phred ScoreChart context menuExport PlotMean Quality Scores0204060801001201400510152025303540Created with MultiQC

        Per Sequence Quality Scores
        24
        0
        0

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

        Created with Highcharts 5.0.6Mean Sequence Quality (Phred Score)CountChart context menuExport PlotPer Sequence Quality Scores0510152025303505M10M15M20M25MCreated with MultiQC

        Per Base Sequence Content
        0
        0
        24

        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
        0
        0
        24

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

        Created with Highcharts 5.0.6%GCCountChart context menuExport PlotPer Sequence GC Content0102030405060708090100012345678Created with MultiQC

        Per Base N Content
        24
        0
        0

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

        Created with Highcharts 5.0.6Position in Read (bp)Percentage N-CountChart context menuExport PlotPer Base N Content0204060801001201400123456Created with MultiQC

        Sequence Length Distribution
        24
        0
        0

        All samples have sequences of a single length (150bp).

        Sequence Duplication Levels
        0
        0
        24

        The relative level of duplication found for every sequence. See the FastQC help.

        Created with Highcharts 5.0.6Sequence Duplication Level% of LibraryChart context menuExport PlotSequence Duplication Levels123456789>10>50>100>500>1k>5k>10k+020406080100Created with MultiQC

        Overrepresented sequences
        0
        16
        8

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

        Created with Highcharts 5.0.6Percentage of Total SequencesChart context menuExport PlotOverrepresented sequencesTop over-represented sequenceSum of remaining over-represented sequencesHJT2TBGX5_n01_2a_t4d9aHJT2TBGX5_n01_2a_t4d9bHJT2TBGX5_n01_2a_t6d14bHJT2TBGX5_n01_2b_c1d9aHJT2TBGX5_n01_2b_c1d9bHJT2TBGX5_n01_2b_c2d9aHJT2TBGX5_n01_2b_c2d9bHJT2TBGX5_n01_2b_t1d9aHJT2TBGX5_n01_2b_t1d9bHJT2TBGX5_n01_2b_t2d9aHJT2TBGX5_n01_2b_t3d14aHJT2TBGX5_n01_2b_t4d14aHJT2TBGX5_n02_2a_t4d9aHJT2TBGX5_n02_2a_t4d9bHJT2TBGX5_n02_2a_t6d14bHJT2TBGX5_n02_2b_c1d9aHJT2TBGX5_n02_2b_c1d9bHJT2TBGX5_n02_2b_c2d9aHJT2TBGX5_n02_2b_c2d9bHJT2TBGX5_n02_2b_t1d9aHJT2TBGX5_n02_2b_t1d9bHJT2TBGX5_n02_2b_t2d9aHJT2TBGX5_n02_2b_t3d14aHJT2TBGX5_n02_2b_t4d14a0%2%4%6%8%10%12%14%16%18%20%22%Created with MultiQC

        Adapter Content
        0
        0
        24

        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.

        Created with Highcharts 5.0.6Position% of SequencesChart context menuExport PlotAdapter Content02040608010012002.557.51012.51517.520Created with MultiQC

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

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