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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 1.11

        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 2022-11-11, 17:31 based on data in:

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

        General Statistics

        Showing 20/20 rows and 6/8 columns.
        Sample Name% mCpG% mCHG% mCHHM C's% Dups% Aligned
        CH01_06_S1_R1
        74.2%
        1.2%
        6.5%
        120.5
        35.1%
        50.3%
        CH01_14_S2_R1
        68.6%
        1.6%
        12.0%
        83.6
        40.8%
        46.6%
        CH01_22_S3_R1
        67.1%
        1.2%
        7.7%
        134.2
        38.0%
        50.9%
        CH01_38_S4_R1
        68.9%
        1.6%
        11.4%
        88.6
        32.1%
        46.7%
        CH03_04_S5_R1
        12.2%
        2.5%
        35.3%
        64.9
        25.1%
        31.3%
        CH03_15_S6_R1
        20.9%
        1.5%
        18.3%
        79.0
        37.7%
        30.7%
        CH03_33_S7_R1
        73.6%
        1.1%
        5.3%
        127.5
        35.9%
        50.5%
        CH05_01_S8_R1
        52.9%
        2.0%
        25.6%
        91.9
        27.9%
        40.3%
        CH05_06_S9_R1
        7.5%
        1.4%
        16.3%
        57.8
        46.0%
        29.6%
        CH05_21_S10_R1
        65.0%
        1.3%
        11.8%
        112.5
        36.0%
        50.6%
        CH05_24_S11_R1
        72.4%
        1.5%
        13.0%
        142.0
        34.7%
        50.4%
        CH07_06_S12_R1
        65.5%
        1.3%
        8.5%
        125.1
        34.5%
        48.6%
        CH07_11_S13_R1
        8.3%
        1.6%
        12.7%
        74.6
        41.2%
        30.6%
        CH07_24_S14_R1
        7.5%
        1.6%
        13.7%
        77.5
        46.5%
        33.6%
        CH09_02_S15_R1
        69.2%
        1.8%
        14.7%
        85.8
        31.7%
        45.1%
        CH09_13_S16_R1
        46.9%
        1.9%
        18.7%
        54.3
        75.8%
        50.9%
        CH09_28_S17_R1
        68.7%
        1.7%
        7.3%
        109.0
        34.1%
        50.3%
        CH10_01_S18_R1
        71.6%
        1.4%
        7.1%
        97.4
        29.1%
        52.0%
        CH10_08_S19_R1
        32.7%
        1.8%
        26.2%
        73.7
        26.1%
        38.4%
        CH10_11_S20_R1
        68.5%
        1.5%
        11.6%
        98.7
        31.7%
        48.4%

        Bismark

        Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

        Alignment Rates

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotBismark: Alignment ScoresAligned UniquelyAligned AmbiguouslyDid Not AlignNo Genomic SequenceCH01_06_S1_R1CH01_14_S2_R1CH01_22_S3_R1CH01_38_S4_R1CH03_04_S5_R1CH03_15_S6_R1CH03_33_S7_R1CH05_01_S8_R1CH05_06_S9_R1CH05_21_S10_R1CH05_24_S11_R1CH07_06_S12_R1CH07_11_S13_R1CH07_24_S14_R1CH09_02_S15_R1CH09_13_S16_R1CH09_28_S17_R1CH10_01_S18_R1CH10_08_S19_R1CH10_11_S20_R1010M20M2.5M5M7.5M12.5M15M17.5M22.5M25M27.5MCreated with MultiQC

        Deduplication

        Created with Highcharts 5.0.6% ReadsChart context menuExport PlotBismark: DeduplicationDeduplicated reads (remaining)Duplicate reads (removed)CH01_06_S1_R1CH01_14_S2_R1CH01_22_S3_R1CH01_38_S4_R1CH03_04_S5_R1CH03_15_S6_R1CH03_33_S7_R1CH05_01_S8_R1CH05_06_S9_R1CH05_21_S10_R1CH05_24_S11_R1CH07_06_S12_R1CH07_11_S13_R1CH07_24_S14_R1CH09_02_S15_R1CH09_13_S16_R1CH09_28_S17_R1CH10_01_S18_R1CH10_08_S19_R1CH10_11_S20_R10102030405060708090100Created with MultiQC

        Strand Alignment

        Created with Highcharts 5.0.6% ReadsChart context menuExport PlotBismark: Alignment to Individual Bisulfite StrandsOriginal bottom strandComplementary to original bottom strandComplementary to original top strandOriginal top strandCH01_06_S1_R1CH01_14_S2_R1CH01_22_S3_R1CH01_38_S4_R1CH03_04_S5_R1CH03_15_S6_R1CH03_33_S7_R1CH05_01_S8_R1CH05_06_S9_R1CH05_21_S10_R1CH05_24_S11_R1CH07_06_S12_R1CH07_11_S13_R1CH07_24_S14_R1CH09_02_S15_R1CH09_13_S16_R1CH09_28_S17_R1CH10_01_S18_R1CH10_08_S19_R1CH10_11_S20_R10102030405060708090100Created with MultiQC

        Cytosine Methylation

        Hover over a data point for more information
        Created with Highcharts 5.0.60255075100Methylated CpG
        Created with Highcharts 5.0.60255075100Methylated CHG
        Created with Highcharts 5.0.60255075100Methylated CHH

        M-Bias

        This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

        Created with Highcharts 5.0.6Position (bp)% MethylationChart context menuExport PlotBismark: M-Bias0102030405060708090100110120130020406080100Created with MultiQC