P9658: M.Dopson_17_06

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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in M.Dopson_17_06_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 1.5

        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

        P9658: M.Dopson_17_06
        sysmetex_leaching_manuscript_LNU_samples

        Contact E-mail:
        stephan.christel@lnu.se
        Application Type:
        RNA-seq
        Library Method:
        RNA, Illumina TruSeq Stranded mRNA, no depletion or selection, -, 1529
        Sequencing Platform:
        HiSeq 2500 High Output V4
        Sequencing Setup:
        2x125
        Reference Genome:
        Multiple (-, -)

        Report generated on 2018-04-12, 10:35 based on data in: /lupus/proj/ngi2016003/nobackup/NGI/ANALYSIS/P9658/qc_ngi


        General Statistics

        Showing 48/48 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        P9658_101_S68_L003_R1_001_ACBKUTANXX
        83.5%
        54%
        26.8
        P9658_101_S68_L003_R2_001_ACBKUTANXX
        84.2%
        54%
        26.8
        P9658_101_S68_L004_R1_001_ACBKUTANXX
        83.9%
        54%
        26.9
        P9658_101_S68_L004_R2_001_ACBKUTANXX
        83.8%
        54%
        26.9
        P9658_102_S69_L003_R1_001_ACBKUTANXX
        81.6%
        54%
        20.8
        P9658_102_S69_L003_R2_001_ACBKUTANXX
        81.5%
        54%
        20.8
        P9658_102_S69_L004_R1_001_ACBKUTANXX
        81.6%
        54%
        20.7
        P9658_102_S69_L004_R2_001_ACBKUTANXX
        80.8%
        54%
        20.7
        P9658_103_S70_L003_R1_001_ACBKUTANXX
        81.8%
        54%
        19.9
        P9658_103_S70_L003_R2_001_ACBKUTANXX
        81.9%
        54%
        19.9
        P9658_103_S70_L004_R1_001_ACBKUTANXX
        82.2%
        54%
        20.2
        P9658_103_S70_L004_R2_001_ACBKUTANXX
        81.8%
        54%
        20.2
        P9658_104_S71_L003_R1_001_ACBKUTANXX
        79.6%
        54%
        21.9
        P9658_104_S71_L003_R2_001_ACBKUTANXX
        80.4%
        54%
        21.9
        P9658_104_S71_L004_R1_001_ACBKUTANXX
        80.1%
        54%
        22.2
        P9658_104_S71_L004_R2_001_ACBKUTANXX
        79.7%
        54%
        22.2
        P9658_105_S72_L003_R1_001_ACBKUTANXX
        79.8%
        55%
        18.1
        P9658_105_S72_L003_R2_001_ACBKUTANXX
        80.4%
        55%
        18.1
        P9658_105_S72_L004_R1_001_ACBKUTANXX
        80.1%
        55%
        18.2
        P9658_105_S72_L004_R2_001_ACBKUTANXX
        79.5%
        55%
        18.2
        P9658_106_S73_L003_R1_001_ACBKUTANXX
        85.7%
        53%
        20.0
        P9658_106_S73_L003_R2_001_ACBKUTANXX
        85.8%
        53%
        20.0
        P9658_106_S73_L004_R1_001_ACBKUTANXX
        86.0%
        53%
        20.1
        P9658_106_S73_L004_R2_001_ACBKUTANXX
        85.4%
        53%
        20.1
        P9658_107_S74_L003_R1_001_ACBKUTANXX
        87.0%
        54%
        20.1
        P9658_107_S74_L003_R2_001_ACBKUTANXX
        86.6%
        54%
        20.1
        P9658_107_S74_L004_R1_001_ACBKUTANXX
        87.3%
        54%
        20.1
        P9658_107_S74_L004_R2_001_ACBKUTANXX
        85.7%
        54%
        20.1
        P9658_108_S75_L003_R1_001_ACBKUTANXX
        86.7%
        53%
        20.5
        P9658_108_S75_L003_R2_001_ACBKUTANXX
        86.1%
        52%
        20.5
        P9658_108_S75_L004_R1_001_ACBKUTANXX
        86.9%
        53%
        20.6
        P9658_108_S75_L004_R2_001_ACBKUTANXX
        85.5%
        52%
        20.6
        P9658_109_S76_L003_R1_001_ACBKUTANXX
        92.5%
        54%
        35.7
        P9658_109_S76_L003_R2_001_ACBKUTANXX
        91.8%
        54%
        35.7
        P9658_109_S76_L004_R1_001_ACBKUTANXX
        92.9%
        54%
        35.7
        P9658_109_S76_L004_R2_001_ACBKUTANXX
        91.7%
        54%
        35.7
        P9658_110_S77_L003_R1_001_ACBKUTANXX
        82.0%
        54%
        27.1
        P9658_110_S77_L003_R2_001_ACBKUTANXX
        82.2%
        54%
        27.1
        P9658_110_S77_L004_R1_001_ACBKUTANXX
        81.9%
        54%
        26.8
        P9658_110_S77_L004_R2_001_ACBKUTANXX
        81.7%
        54%
        26.8
        P9658_111_S78_L003_R1_001_ACBKUTANXX
        80.7%
        54%
        22.7
        P9658_111_S78_L003_R2_001_ACBKUTANXX
        80.7%
        54%
        22.7
        P9658_111_S78_L004_R1_001_ACBKUTANXX
        81.1%
        54%
        22.9
        P9658_111_S78_L004_R2_001_ACBKUTANXX
        80.2%
        54%
        22.9
        P9658_112_S79_L003_R1_001_ACBKUTANXX
        80.2%
        54%
        25.7
        P9658_112_S79_L003_R2_001_ACBKUTANXX
        81.0%
        54%
        25.7
        P9658_112_S79_L004_R1_001_ACBKUTANXX
        80.6%
        54%
        25.9
        P9658_112_S79_L004_R2_001_ACBKUTANXX
        80.0%
        54%
        25.9

        FastQ Screen

        FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

        The reference genome in Genomic status is Multiple (-, -)

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        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 sample 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 (126bp).

        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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