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        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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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.30

        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/MultiQC/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 2026-10-09, 17:19 PDT based on data in:
        • /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/fastp
        • /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark
        • /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/dedup
        • /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation

        General Statistics

        Showing 45/45 rows and 10/14 columns.
        Sample NamemCpGC'sC coverageDupsUniqueAlignedAligned% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% Adapter
        PUM1 (paired)_R1
        5.8%
        96.4%
        10244.1Mb
        76.8M
        18.7%
        98.4%
        9.6%
        PUM2 (paired)_R1
        5.6%
        96.4%
        9865.2Mb
        73.9M
        18.7%
        98.4%
        9.6%
        PUM3 (paired)_R1
        4.9%
        96.4%
        8546.5Mb
        64.0M
        18.7%
        98.4%
        9.6%
        PUM4 (paired)_R1
        3.1%
        96.4%
        8046.3Mb
        60.3M
        18.8%
        98.4%
        10.8%
        PUM5 (paired)_R1
        3.5%
        96.4%
        5982.4Mb
        44.8M
        18.7%
        98.4%
        9.6%
        Pum1_PE_report
        21.5M
        56.0%
        Pum1_pe
        19.4%
        706.7
        3.65X
        7.0%
        20.0M
        Pum2_PE_report
        20.7M
        56.0%
        Pum2_pe
        19.4%
        682.5
        3.52X
        6.8%
        19.3M
        Pum3_PE_report
        17.9M
        56.0%
        Pum3_pe
        19.4%
        597.0
        3.08X
        5.9%
        16.9M
        Pum4_PE_report
        17.0M
        56.2%
        Pum4_pe
        19.2%
        571.0
        3.02X
        3.5%
        16.4M
        Pum5_PE_report
        12.5M
        56.0%
        Pum5_pe
        19.4%
        425.9
        2.20X
        4.2%
        12.0M
        Qui1 (paired)_R1
        5.9%
        96.6%
        10318.7Mb
        77.4M
        18.9%
        98.5%
        14.2%
        Qui1_PE_report
        22.1M
        57.1%
        Qui1_pe
        18.9%
        681.6
        3.89X
        7.0%
        20.6M
        Qui2 (paired)_R1
        5.2%
        96.0%
        9728.7Mb
        73.3M
        18.8%
        98.3%
        10.9%
        Qui2_PE_report
        20.9M
        57.0%
        Qui2_pe
        21.6%
        652.7
        3.56X
        6.4%
        19.5M
        Qui3 (paired)_R1
        6.0%
        96.4%
        11038.5Mb
        82.9M
        18.7%
        98.4%
        12.2%
        Qui3_PE_report
        23.8M
        57.4%
        Qui3_pe
        20.5%
        740.4
        4.08X
        7.1%
        22.1M
        Qui4 (paired)_R1
        4.5%
        96.2%
        9142.3Mb
        68.9M
        19.0%
        98.3%
        14.2%
        Qui4_PE_report
        19.7M
        57.3%
        Qui4_pe
        19.3%
        611.5
        3.48X
        5.3%
        18.7M
        Qui5 (paired)_R1
        5.1%
        96.6%
        8833.9Mb
        66.3M
        18.9%
        98.5%
        14.2%
        Qui5_PE_report
        18.9M
        57.1%
        Qui5_pe
        18.9%
        590.0
        3.36X
        6.1%
        17.8M
        RP1 (paired)_R1
        5.3%
        96.4%
        11108.5Mb
        83.0M
        18.8%
        98.5%
        9.7%
        RP2 (paired)_R1
        5.1%
        96.3%
        9532.6Mb
        71.6M
        18.8%
        98.2%
        11.0%
        RP3 (paired)_R1
        3.9%
        96.3%
        8697.3Mb
        65.5M
        18.9%
        98.2%
        14.3%
        RP4 (paired)_R1
        4.3%
        96.3%
        10671.9Mb
        79.9M
        18.8%
        98.5%
        11.4%
        RP5 (paired)_R1
        3.9%
        96.3%
        8697.3Mb
        65.5M
        18.9%
        98.2%
        14.3%
        Rio1_PE_report
        24.3M
        58.5%
        Rio1_pe
        20.3%
        788.0
        4.25X
        6.4%
        22.7M
        Rio2_PE_report
        20.5M
        57.4%
        Rio2_pe
        20.1%
        662.1
        3.59X
        6.2%
        19.3M
        Rio3_PE_report
        18.9M
        57.7%
        Rio3_pe
        21.1%
        574.3
        3.27X
        4.8%
        18.0M
        Rio4_PE_report
        23.2M
        58.0%
        Rio4_pe
        20.5%
        744.0
        4.11X
        5.0%
        22.0M
        Rio5_PE_report
        18.9M
        57.7%
        Rio5_pe
        21.1%
        574.3
        3.27X
        4.8%
        18.0M

        Bismark

        Version: 0.25.1

        Maps bisulfite converted sequence reads and determine cytosine methylation states.URL: http://www.bioinformatics.babraham.ac.uk/projects/bismarkDOI: 10.1093/bioinformatics/btr167

        Alignment Rates

        Created with MultiQC

        Deduplication

        Created with MultiQC

        Strand Alignment

        All samples were run with --directional mode; alignments to complementary strands (CTOT, CTOB) were ignored.

        Created with MultiQC

        Cytosine Methylation

        Created with MultiQC

        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 MultiQC

        fastp

        Version: 1.0.1

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bismark0.25.1
        fastp1.0.1

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.