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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 1.5.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 2018-05-18, 08:34 based on data in: /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc


        General Statistics

        Showing 104/104 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        EPI-103_S27_L005_R1_001_val_1
        16.3%
        24%
        93 bp
        20.3
        EPI-103_S27_L005_R2_001_val_2
        21.5%
        24%
        92 bp
        20.3
        EPI-104_S28_L005_R1_001_val_1
        16.6%
        24%
        91 bp
        30.0
        EPI-104_S28_L005_R2_001_val_2
        22.8%
        23%
        90 bp
        30.0
        EPI-111_S29_L005_R1_001_val_1
        16.3%
        23%
        90 bp
        27.0
        EPI-111_S29_L005_R2_001_val_2
        22.1%
        23%
        89 bp
        27.0
        EPI-113_S30_L005_R1_001_val_1
        18.7%
        24%
        91 bp
        26.3
        EPI-113_S30_L005_R2_001_val_2
        24.9%
        23%
        90 bp
        26.3
        EPI-119_S31_L005_R1_001_val_1
        19.7%
        24%
        92 bp
        28.9
        EPI-119_S31_L005_R2_001_val_2
        26.3%
        24%
        91 bp
        28.9
        EPI-120_S32_L005_R1_001_val_1
        16.3%
        23%
        92 bp
        24.1
        EPI-120_S32_L005_R2_001_val_2
        22.6%
        23%
        91 bp
        24.1
        EPI-127_S33_L005_R1_001_val_1
        18.1%
        24%
        92 bp
        22.3
        EPI-127_S33_L005_R2_001_val_2
        24.1%
        23%
        91 bp
        22.3
        EPI-128_S34_L005_R1_001_val_1
        18.8%
        24%
        91 bp
        24.6
        EPI-128_S34_L005_R2_001_val_2
        24.9%
        23%
        90 bp
        24.6
        EPI-135_S35_L005_R1_001_val_1
        19.2%
        24%
        87 bp
        28.7
        EPI-135_S35_L005_R2_001_val_2
        25.6%
        24%
        87 bp
        28.7
        EPI-136_S36_L005_R1_001_val_1
        17.3%
        24%
        88 bp
        27.8
        EPI-136_S36_L005_R2_001_val_2
        23.3%
        24%
        87 bp
        27.8
        EPI-143_S37_L005_R1_001_val_1
        16.5%
        24%
        91 bp
        21.2
        EPI-143_S37_L005_R2_001_val_2
        21.4%
        24%
        90 bp
        21.2
        EPI-145_S38_L005_R1_001_val_1
        19.1%
        24%
        91 bp
        25.3
        EPI-145_S38_L005_R2_001_val_2
        25.4%
        23%
        90 bp
        25.3
        EPI-151_S2_L002_R1_001_val_1
        27.6%
        25%
        91 bp
        24.5
        EPI-151_S2_L002_R2_001_val_2
        34.1%
        25%
        90 bp
        24.5
        EPI-152_S3_L002_R1_001_val_1
        28.1%
        25%
        91 bp
        29.9
        EPI-152_S3_L002_R2_001_val_2
        34.3%
        25%
        90 bp
        29.9
        EPI-153_S4_L002_R1_001_val_1
        35.0%
        25%
        88 bp
        26.0
        EPI-153_S4_L002_R2_001_val_2
        40.0%
        25%
        87 bp
        26.0
        EPI-154_S5_L002_R1_001_val_1
        27.1%
        25%
        90 bp
        25.2
        EPI-154_S5_L002_R2_001_val_2
        32.3%
        25%
        89 bp
        25.2
        EPI-159_S6_L002_R1_001_val_1
        27.6%
        25%
        90 bp
        15.5
        EPI-159_S6_L002_R2_001_val_2
        31.1%
        25%
        89 bp
        15.5
        EPI-160_S7_L002_R1_001_val_1
        26.6%
        25%
        84 bp
        31.9
        EPI-160_S7_L002_R2_001_val_2
        31.8%
        25%
        84 bp
        31.9
        EPI-161_S8_L002_R1_001_val_1
        25.0%
        25%
        85 bp
        24.5
        EPI-161_S8_L002_R2_001_val_2
        28.1%
        25%
        85 bp
        24.5
        EPI-162_S9_L002_R1_001_val_1
        21.3%
        25%
        84 bp
        22.8
        EPI-162_S9_L002_R2_001_val_2
        25.0%
        25%
        83 bp
        22.8
        EPI-167_S10_L002_R1_001_val_1
        26.5%
        24%
        92 bp
        24.5
        EPI-167_S10_L002_R2_001_val_2
        31.2%
        24%
        91 bp
        24.5
        EPI-168_S11_L002_R1_001_val_1
        27.6%
        25%
        91 bp
        22.7
        EPI-168_S11_L002_R2_001_val_2
        33.9%
        25%
        90 bp
        22.7
        EPI-169_S12_L002_R1_001_val_1
        23.2%
        25%
        85 bp
        21.4
        EPI-169_S12_L002_R2_001_val_2
        27.9%
        26%
        84 bp
        21.4
        EPI-170_S13_L002_R1_001_val_1
        23.5%
        25%
        83 bp
        28.0
        EPI-170_S13_L002_R2_001_val_2
        27.6%
        25%
        83 bp
        28.0
        EPI-175_S14_L003_R1_001_val_1
        23.1%
        25%
        90 bp
        24.7
        EPI-175_S14_L003_R2_001_val_2
        29.2%
        25%
        89 bp
        24.7
        EPI-176_S15_L003_R1_001_val_1
        27.1%
        25%
        90 bp
        36.3
        EPI-176_S15_L003_R2_001_val_2
        32.2%
        25%
        89 bp
        36.3
        EPI-181_S16_L003_R1_001_val_1
        25.5%
        25%
        91 bp
        27.2
        EPI-181_S16_L003_R2_001_val_2
        31.9%
        25%
        90 bp
        27.2
        EPI-182_S17_L003_R1_001_val_1
        23.1%
        24%
        90 bp
        31.5
        EPI-182_S17_L003_R2_001_val_2
        28.8%
        24%
        90 bp
        31.5
        EPI-184_S18_L003_R1_001_val_1
        25.1%
        25%
        87 bp
        20.7
        EPI-184_S18_L003_R2_001_val_2
        29.8%
        25%
        86 bp
        20.7
        EPI-185_S19_L003_R1_001_val_1
        31.7%
        26%
        89 bp
        11.0
        EPI-185_S19_L003_R2_001_val_2
        34.0%
        26%
        88 bp
        11.0
        EPI-187_S20_L003_R1_001_val_1
        26.6%
        25%
        89 bp
        22.7
        EPI-187_S20_L003_R2_001_val_2
        33.2%
        25%
        88 bp
        22.7
        EPI-188_S21_L003_R1_001_val_1
        25.7%
        25%
        81 bp
        21.5
        EPI-188_S21_L003_R2_001_val_2
        29.2%
        25%
        80 bp
        21.5
        EPI-193_S22_L003_R1_001_val_1
        22.5%
        25%
        83 bp
        26.8
        EPI-193_S22_L003_R2_001_val_2
        27.5%
        25%
        82 bp
        26.8
        EPI-194_S23_L003_R1_001_val_1
        23.2%
        25%
        92 bp
        27.5
        EPI-194_S23_L003_R2_001_val_2
        31.3%
        25%
        91 bp
        27.5
        EPI-199_S24_L003_R1_001_val_1
        28.6%
        26%
        85 bp
        15.9
        EPI-199_S24_L003_R2_001_val_2
        32.6%
        26%
        84 bp
        15.9
        EPI-200_S25_L003_R1_001_val_1
        26.2%
        25%
        82 bp
        25.1
        EPI-200_S25_L003_R2_001_val_2
        31.6%
        25%
        82 bp
        25.1
        EPI-205_S26_L004_R1_001_val_1
        24.7%
        26%
        79 bp
        16.5
        EPI-205_S26_L004_R2_001_val_2
        27.4%
        26%
        79 bp
        16.5
        EPI-206_S27_L004_R1_001_val_1
        23.1%
        25%
        82 bp
        20.9
        EPI-206_S27_L004_R2_001_val_2
        27.4%
        25%
        81 bp
        20.9
        EPI-208_S28_L004_R1_001_val_1
        23.0%
        25%
        79 bp
        29.1
        EPI-208_S28_L004_R2_001_val_2
        25.8%
        25%
        78 bp
        29.1
        EPI-209_S29_L004_R1_001_val_1
        28.1%
        25%
        86 bp
        29.6
        EPI-209_S29_L004_R2_001_val_2
        34.4%
        25%
        86 bp
        29.6
        EPI-214_S30_L004_R1_001_val_1
        24.2%
        25%
        88 bp
        28.7
        EPI-214_S30_L004_R2_001_val_2
        28.2%
        25%
        87 bp
        28.7
        EPI-215_S31_L004_R1_001_val_1
        27.5%
        25%
        83 bp
        21.2
        EPI-215_S31_L004_R2_001_val_2
        32.3%
        25%
        83 bp
        21.2
        EPI-220_S32_L004_R1_001_val_1
        31.5%
        25%
        87 bp
        15.7
        EPI-220_S32_L004_R2_001_val_2
        34.1%
        25%
        86 bp
        15.7
        EPI-221_S33_L004_R1_001_val_1
        28.0%
        25%
        83 bp
        16.3
        EPI-221_S33_L004_R2_001_val_2
        31.0%
        25%
        82 bp
        16.3
        EPI-226_S34_L004_R1_001_val_1
        26.7%
        25%
        90 bp
        11.1
        EPI-226_S34_L004_R2_001_val_2
        30.2%
        25%
        89 bp
        11.1
        EPI-227_S35_L004_R1_001_val_1
        26.1%
        25%
        86 bp
        13.5
        EPI-227_S35_L004_R2_001_val_2
        29.3%
        25%
        85 bp
        13.5
        EPI-229_S36_L004_R1_001_val_1
        25.5%
        25%
        85 bp
        19.9
        EPI-229_S36_L004_R2_001_val_2
        29.4%
        25%
        85 bp
        19.9
        EPI-230_S37_L004_R1_001_val_1
        33.3%
        25%
        85 bp
        29.4
        EPI-230_S37_L004_R2_001_val_2
        35.8%
        25%
        84 bp
        29.4
        EPI-41_S38_L005_R1_001_val_1
        34.3%
        25%
        84 bp
        25.1
        EPI-41_S38_L005_R2_001_val_2
        36.8%
        25%
        84 bp
        25.1
        EPI-42_S39_L005_R1_001_val_1
        32.2%
        25%
        84 bp
        29.6
        EPI-42_S39_L005_R2_001_val_2
        38.0%
        25%
        83 bp
        29.6
        EPI-43_S40_L005_R1_001_val_1
        33.7%
        25%
        85 bp
        22.6
        EPI-43_S40_L005_R2_001_val_2
        37.5%
        25%
        84 bp
        22.6
        EPI-44_S41_L005_R1_001_val_1
        31.1%
        25%
        83 bp
        13.8
        EPI-44_S41_L005_R2_001_val_2
        34.8%
        25%
        83 bp
        13.8

        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        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.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

        104 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.

        No samples found with any adapter contamination > 0.1%