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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.

         Loading report..

        Report generated on 2017-10-31, 18:10 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HWCGKBGX3/merged

        General Statistics

        Showing 20/20 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        HWCGKBGX3_n01_ap_37
        52.9%
        45%
        66.8
        HWCGKBGX3_n01_ap_38
        48.2%
        45%
        37.7
        HWCGKBGX3_n01_ap_39
        42.1%
        45%
        26.0
        HWCGKBGX3_n01_ap_4
        42.9%
        44%
        29.1
        HWCGKBGX3_n01_ap_40
        44.7%
        45%
        28.3
        HWCGKBGX3_n01_ap_41
        40.0%
        44%
        20.0
        HWCGKBGX3_n01_ap_42
        41.3%
        45%
        19.3
        HWCGKBGX3_n01_ap_46
        38.1%
        43%
        18.2
        HWCGKBGX3_n01_ap_47
        54.2%
        43%
        77.8
        HWCGKBGX3_n01_ap_48
        1.1%
        44%
        0.0
        HWCGKBGX3_n01_ap_5
        35.8%
        44%
        11.9
        HWCGKBGX3_n01_ap_6
        46.5%
        44%
        40.1
        HWCGKBGX3_n01_ap_79
        40.3%
        45%
        14.5
        HWCGKBGX3_n01_ap_80
        44.2%
        46%
        18.1
        HWCGKBGX3_n01_ap_81
        56.4%
        46%
        49.4
        HWCGKBGX3_n01_ap_82
        42.7%
        44%
        20.3
        HWCGKBGX3_n01_ap_83
        34.2%
        45%
        11.6
        HWCGKBGX3_n01_ap_83_old
        61.6%
        44%
        91.9
        HWCGKBGX3_n01_ap_84
        43.6%
        44%
        19.3
        HWCGKBGX3_n01_ap_84_old
        3.2%
        44%
        0.1

        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
        1011268525
        613876708
        2.2
        0.12%

        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 20/20 rows and 3/3 columns.
        LibraryTotal Read CountPortion (%)Perfect (%)
        ap_80
        18098760
        3.0
        95.7
        ap_82
        20344046
        3.4
        95.5
        ap_79
        14530883
        2.4
        94.7
        ap_6
        40074138
        6.7
        96.5
        ap_42
        19322849
        3.2
        95.8
        ap_46
        18178099
        3.0
        95.1
        ap_83_old
        91867971
        15.3
        95.9
        ap_81
        49395384
        8.2
        94.0
        ap_84
        19307543
        3.2
        95.5
        ap_48
        34720
        0.0
        39.8
        ap_84_old
        100935
        0.0
        3.6
        ap_40
        28278356
        4.7
        82.2
        ap_41
        19991116
        3.3
        96.4
        ap_5
        11860758
        2.0
        95.9
        ap_39
        26038344
        4.3
        96.2
        ap_38
        37727930
        6.3
        95.6
        ap_4
        29066191
        4.8
        96.2
        ap_83
        11566867
        1.9
        95.6
        ap_37
        66826778
        11.1
        94.8
        ap_47
        77787175
        13.0
        95.6

        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.

        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 (75bp).

        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.

        loading..

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

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