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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 1.8

        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 2021-07-14, 11:20 based on data in: /gscratch/scrubbed/samwhite/outputs/20210714_cvir_gonad_RNAseq_fastp_trimming

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

        General Statistics

        Showing 26/26 rows and 4/6 columns.
        Sample Name% DuplicationGC content% PF% Adapter
        S12M_R1
        5.0%
        39.9%
        90.3%
        64.9%
        S13M_R1
        4.9%
        41.0%
        79.0%
        72.9%
        S16F_R1
        6.2%
        42.7%
        98.4%
        52.5%
        S19F_R1
        6.6%
        42.2%
        98.5%
        61.5%
        S22F_R1
        7.3%
        41.6%
        98.7%
        65.4%
        S23M_R1
        5.3%
        39.8%
        88.5%
        80.6%
        S29F_R1
        5.4%
        41.2%
        98.4%
        65.1%
        S31M_R1
        4.8%
        37.9%
        97.8%
        45.2%
        S35F_R1
        5.6%
        41.9%
        98.6%
        64.8%
        S36F_R1
        6.2%
        41.4%
        98.5%
        63.8%
        S39F_R1
        6.2%
        42.0%
        98.5%
        64.6%
        S3F_R1
        5.9%
        41.5%
        98.5%
        61.0%
        S41F_R1
        6.1%
        42.0%
        98.5%
        63.4%
        S44F_R1
        6.4%
        42.9%
        98.4%
        57.7%
        S48M_R1
        7.0%
        40.0%
        80.8%
        74.2%
        S50F_R1
        5.5%
        42.3%
        98.7%
        62.6%
        S52F_R1
        5.3%
        40.7%
        98.7%
        58.6%
        S53F_R1
        5.9%
        41.7%
        98.3%
        69.2%
        S54F_R1
        6.3%
        41.7%
        98.5%
        69.0%
        S59M_R1
        5.5%
        39.7%
        97.5%
        56.3%
        S64M_R1
        6.0%
        41.5%
        98.0%
        49.7%
        S6M_R1
        4.9%
        40.2%
        81.9%
        71.1%
        S76F_R1
        6.8%
        43.1%
        98.5%
        63.2%
        S77F_R1
        7.6%
        43.2%
        98.6%
        60.0%
        S7M_R1
        4.5%
        40.1%
        89.7%
        62.5%
        S9M_R1
        4.3%
        39.8%
        85.4%
        67.5%

        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotFastp: Filtered ReadsPassed FilterLow QualityToo Many NToo shortS12M_R1S16F_R1S22F_R1S29F_R1S35F_R1S39F_R1S41F_R1S48M_R1S52F_R1S54F_R1S64M_R1S76F_R1S7M_R1010M20M30M40M50M60M70M80M90M100M110M120M130M140M15…150MCreated with MultiQC

        Duplication Rates

        Duplication rates of sampled reads.

        Created with Highcharts 5.0.6Duplication levelRead percentChart context menuExport PlotFastp: Duplication Rate246810121416182022242628300%20%40%60%80%100%Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with Highcharts 5.0.6Insert sizeRead percentChart context menuExport PlotFastp: Insert Size Distribution02550751001251501752002252500%0.25%0.5%0.75%1%1.25%1.5%Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Sequence QualityChart context menuExport PlotFastp: Sequence Quality0204060801001201400510152025303540Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Base Content PercentChart context menuExport PlotFastp: Read GC Content0204060801001201400%20%40%60%80%100%Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Base Content PercentChart context menuExport PlotFastp: Read N Content0204060801001201400%1%2%3%4%5%6%Created with MultiQC