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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 2019-04-24, 17:04 based on data in: /beegfs/mk5636/logs/html/CCRMBACXX/3


        General Statistics

        Showing 20/20 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        CCRMBACXX_l03_n01_A2S1
        64.6%
        52%
        19.9
        CCRMBACXX_l03_n01_A2S2
        67.7%
        52%
        26.9
        CCRMBACXX_l03_n01_A2S3
        65.9%
        53%
        23.9
        CCRMBACXX_l03_n01_A2S4
        64.5%
        53%
        23.2
        CCRMBACXX_l03_n01_A2S5
        68.5%
        53%
        26.6
        CCRMBACXX_l03_n01_A2S6
        62.0%
        51%
        20.4
        CCRMBACXX_l03_n01_A2S7
        61.8%
        52%
        17.0
        CCRMBACXX_l03_n01_A2S8
        59.2%
        51%
        20.1
        CCRMBACXX_l03_n01_A2S9
        65.0%
        52%
        18.8
        CCRMBACXX_l03_n01_undetermined
        89.6%
        45%
        17.7
        CCRMBACXX_l03_n02_A2S1
        67.3%
        54%
        19.9
        CCRMBACXX_l03_n02_A2S2
        70.4%
        54%
        26.9
        CCRMBACXX_l03_n02_A2S3
        68.9%
        55%
        23.9
        CCRMBACXX_l03_n02_A2S4
        67.8%
        55%
        23.2
        CCRMBACXX_l03_n02_A2S5
        71.1%
        55%
        26.6
        CCRMBACXX_l03_n02_A2S6
        64.5%
        53%
        20.4
        CCRMBACXX_l03_n02_A2S7
        64.5%
        54%
        17.0
        CCRMBACXX_l03_n02_A2S8
        61.9%
        53%
        20.1
        CCRMBACXX_l03_n02_A2S9
        67.6%
        54%
        18.8
        CCRMBACXX_l03_n02_undetermined
        89.6%
        46%
        17.7

        Lane 3 Demultiplexing Report

        Lane 3 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 10/10 rows and 2/2 columns.
        Sample NameTotal Read CountPortion (%)
        undetermined_library
        17,746,396
        8.3
        A2S1
        19,859,729
        9.3
        A2S2
        26,895,663
        12.5
        A2S3
        23,881,124
        11.1
        A2S4
        23,164,110
        10.8
        A2S5
        26,648,641
        12.4
        A2S6
        20,389,729
        9.5
        A2S7
        16,965,132
        7.9
        A2S8
        20,092,558
        9.4
        A2S9
        18,788,117
        8.8

        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 (%)
        NNNNNN
        149859.0
        0.8
        TAGGCA
        66033.0
        0.4
        CCCCCC
        65836.0
        0.4
        GATGTA
        57716.0
        0.3
        GCCCAA
        51961.0
        0.3
        CGGCCC
        51459.0
        0.3
        GACCAA
        50819.0
        0.3
        GACAAC
        49649.0
        0.3
        CGCCCC
        49108.0
        0.3
        GACCAC
        47923.0
        0.3
        CCGCCC
        44717.0
        0.2
        CCGCTC
        42291.0
        0.2
        TGCCCC
        42173.0
        0.2
        CGGCCA
        40478.0
        0.2
        CCCACC
        40346.0
        0.2
        CAGCCC
        40190.0
        0.2
        GAGCAC
        39252.0
        0.2
        CACCCC
        38601.0
        0.2
        GAGAAG
        37616.0
        0.2
        CACCAC
        37610.0
        0.2

        Lane Statistics

        Lane Statistics

        Showing 1/1 rows and 4/4 columns.
        Sample NameTotal # of Single-End ReadsTotal # PF Reads% Undetermined % PhiX Aligned
        3.0
        223,404,656
        214,431,199
        8.3
        8.4

        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

        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.

        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.

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