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        Note that additional data was saved in preQC_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 1.0

        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.

         Loading report..

        Report generated on 2017-11-15, 21:47 based on data in:


        General Statistics

        Showing 176/176 rows and 4/5 columns.
        Sample Name% Dups% GCLengthM Seqs
        ES-0001a_1
        16.6%
        56%
        284 bp
        0.5
        ES-0001a_2
        15.7%
        57%
        285 bp
        0.5
        ES-0001b_1
        27.5%
        57%
        254 bp
        1.2
        ES-0001b_2
        25.9%
        57%
        258 bp
        1.2
        ES-0001c_1
        22.5%
        57%
        278 bp
        0.8
        ES-0001c_2
        18.2%
        59%
        280 bp
        0.8
        ES-0002a_1
        20.7%
        56%
        241 bp
        0.7
        ES-0002a_2
        20.1%
        56%
        242 bp
        0.7
        ES-0002b_1
        23.8%
        57%
        253 bp
        0.9
        ES-0002b_2
        22.3%
        57%
        260 bp
        0.9
        ES-0002c_1
        15.8%
        57%
        281 bp
        0.5
        ES-0002c_2
        13.4%
        57%
        282 bp
        0.5
        ES-0003a_1
        10.8%
        57%
        283 bp
        0.3
        ES-0003a_2
        10.2%
        57%
        283 bp
        0.3
        ES-0003b_1
        24.1%
        57%
        266 bp
        1.0
        ES-0003b_2
        22.6%
        57%
        270 bp
        1.0
        ES-0003c_1
        31.1%
        57%
        266 bp
        1.4
        ES-0003c_2
        29.4%
        57%
        268 bp
        1.4
        ES-0004a_1
        8.6%
        56%
        263 bp
        0.2
        ES-0004a_2
        8.2%
        56%
        264 bp
        0.2
        ES-0004b_1
        23.5%
        57%
        263 bp
        0.9
        ES-0004b_2
        22.2%
        57%
        267 bp
        0.9
        ES-0004c_1
        22.4%
        57%
        276 bp
        0.9
        ES-0004c_2
        20.4%
        57%
        276 bp
        0.9
        ES-0005a_1
        15.8%
        56%
        250 bp
        0.5
        ES-0005a_2
        15.1%
        56%
        251 bp
        0.5
        ES-0005b_1
        23.1%
        57%
        271 bp
        0.9
        ES-0005b_2
        21.6%
        57%
        273 bp
        0.9
        ES-0005c_1
        20.8%
        57%
        279 bp
        0.8
        ES-0005c_2
        18.8%
        57%
        280 bp
        0.8
        ES-0006a_1
        26.6%
        57%
        262 bp
        1.1
        ES-0006a_2
        24.4%
        57%
        266 bp
        1.1
        ES-0006b_1
        25.3%
        57%
        256 bp
        1.0
        ES-0006b_2
        23.8%
        57%
        260 bp
        1.0
        ES-0006c_1
        24.7%
        57%
        268 bp
        1.0
        ES-0006c_2
        23.5%
        57%
        269 bp
        1.0
        ES-0007a_1
        11.9%
        57%
        279 bp
        0.3
        ES-0007a_2
        11.0%
        57%
        280 bp
        0.3
        ES-0007b_1
        31.4%
        57%
        238 bp
        1.4
        ES-0007b_2
        30.1%
        57%
        242 bp
        1.4
        ES-0007c_1
        24.4%
        57%
        273 bp
        0.9
        ES-0007c_2
        19.8%
        59%
        278 bp
        0.9
        ES-0008a_1
        17.6%
        56%
        281 bp
        0.6
        ES-0008a_2
        16.7%
        57%
        282 bp
        0.6
        ES-0008b_1
        18.0%
        57%
        275 bp
        0.6
        ES-0008b_2
        16.7%
        57%
        277 bp
        0.6
        ES-0008c_1
        29.0%
        57%
        264 bp
        1.3
        ES-0008c_2
        27.4%
        57%
        266 bp
        1.3
        ES-0009a_1
        16.8%
        56%
        277 bp
        0.5
        ES-0009a_2
        16.2%
        57%
        278 bp
        0.5
        ES-0009b_1
        24.4%
        57%
        250 bp
        1.0
        ES-0009b_2
        23.1%
        57%
        254 bp
        1.0
        ES-0009c_1
        17.8%
        57%
        258 bp
        0.6
        ES-0009c_2
        15.1%
        59%
        261 bp
        0.6
        ES-0010a_1
        18.9%
        56%
        276 bp
        0.6
        ES-0010a_2
        18.1%
        57%
        277 bp
        0.6
        ES-0010b_1
        23.6%
        57%
        269 bp
        0.9
        ES-0010b_2
        21.9%
        57%
        272 bp
        0.9
        ES-0010c_1
        15.1%
        57%
        274 bp
        0.5
        ES-0010c_2
        11.4%
        59%
        277 bp
        0.5
        ES-0011a_1
        18.2%
        56%
        288 bp
        0.6
        ES-0011a_2
        17.4%
        57%
        288 bp
        0.6
        ES-0011b_1
        20.2%
        57%
        281 bp
        0.7
        ES-0011b_2
        18.1%
        57%
        282 bp
        0.7
        ES-0011c_1
        12.7%
        56%
        265 bp
        0.2
        ES-0011c_2
        10.4%
        58%
        270 bp
        0.2
        ES-0012a_1
        11.7%
        56%
        291 bp
        0.3
        ES-0012a_2
        10.8%
        57%
        292 bp
        0.3
        ES-0012b_1
        18.5%
        57%
        273 bp
        0.6
        ES-0012b_2
        16.9%
        57%
        275 bp
        0.6
        ES-0012c_1
        30.1%
        57%
        235 bp
        1.4
        ES-0012c_2
        28.8%
        57%
        238 bp
        1.4
        ES-0013a_1
        21.8%
        57%
        274 bp
        0.8
        ES-0013a_2
        19.8%
        57%
        276 bp
        0.8
        ES-0013b_1
        22.8%
        57%
        268 bp
        0.8
        ES-0013b_2
        20.9%
        57%
        271 bp
        0.8
        ES-0013c_1
        20.9%
        57%
        274 bp
        0.7
        ES-0013c_2
        17.1%
        59%
        280 bp
        0.7
        ES-0014a_1
        13.8%
        56%
        254 bp
        0.4
        ES-0014a_2
        13.1%
        56%
        255 bp
        0.4
        ES-0014b_1
        21.7%
        57%
        251 bp
        0.8
        ES-0014b_2
        20.6%
        57%
        255 bp
        0.8
        ES-0014c_1
        17.0%
        57%
        283 bp
        0.6
        ES-0014c_2
        14.5%
        57%
        284 bp
        0.6
        ES-0015a_1
        23.2%
        56%
        249 bp
        0.9
        ES-0015a_2
        22.7%
        56%
        250 bp
        0.9
        ES-0015b_1
        25.8%
        57%
        261 bp
        1.1
        ES-0015b_2
        24.6%
        57%
        264 bp
        1.1
        ES-0015c_1
        16.9%
        57%
        276 bp
        0.5
        ES-0015c_2
        12.0%
        59%
        279 bp
        0.5
        ES-0016a_1
        13.9%
        56%
        265 bp
        0.4
        ES-0016a_2
        13.2%
        57%
        266 bp
        0.4
        ES-0016b_1
        23.4%
        56%
        243 bp
        0.9
        ES-0016b_2
        22.3%
        57%
        246 bp
        0.9
        ES-0016c_1
        23.8%
        57%
        264 bp
        0.9
        ES-0016c_2
        22.4%
        57%
        265 bp
        0.9
        ES-0017a_1
        16.2%
        56%
        256 bp
        0.5
        ES-0017a_2
        15.5%
        56%
        257 bp
        0.5
        ES-0017b_1
        19.3%
        57%
        282 bp
        0.7
        ES-0017b_2
        17.5%
        57%
        283 bp
        0.7
        ES-0017c_1
        14.5%
        57%
        265 bp
        0.4
        ES-0017c_2
        10.7%
        59%
        270 bp
        0.4
        ES-0018a_1
        15.8%
        56%
        245 bp
        0.5
        ES-0018a_2
        15.2%
        56%
        246 bp
        0.5
        ES-0018b_1
        19.6%
        56%
        259 bp
        0.7
        ES-0018b_2
        18.1%
        56%
        262 bp
        0.7
        ES-0018c_1
        16.6%
        56%
        273 bp
        0.6
        ES-0018c_2
        14.9%
        57%
        274 bp
        0.6
        ES-0019a_1
        1.8%
        56%
        288 bp
        0.0
        ES-0019a_2
        1.8%
        57%
        288 bp
        0.0
        ES-0019b_1
        18.5%
        57%
        269 bp
        0.7
        ES-0019b_2
        16.8%
        57%
        270 bp
        0.7
        ES-0019c_1
        24.2%
        56%
        231 bp
        1.1
        ES-0019c_2
        23.7%
        57%
        234 bp
        1.1
        ES-0020a_1
        27.2%
        57%
        263 bp
        1.1
        ES-0020a_2
        25.6%
        57%
        267 bp
        1.1
        ES-0020b_1
        26.0%
        57%
        246 bp
        1.0
        ES-0020b_2
        24.9%
        57%
        249 bp
        1.0
        ES-0020c_1
        25.2%
        57%
        273 bp
        1.0
        ES-0020c_2
        23.3%
        57%
        274 bp
        1.0
        ES-0021a_1
        14.7%
        56%
        277 bp
        0.4
        ES-0021a_2
        14.0%
        57%
        277 bp
        0.4
        ES-0021b_1
        26.0%
        57%
        261 bp
        1.0
        ES-0021b_2
        24.4%
        57%
        264 bp
        1.0
        ES-0021c_1
        18.0%
        57%
        284 bp
        0.6
        ES-0021c_2
        15.9%
        57%
        285 bp
        0.6
        ES-0022a_1
        15.8%
        56%
        270 bp
        0.5
        ES-0022a_2
        15.2%
        56%
        271 bp
        0.5
        ES-0022b_1
        22.5%
        57%
        272 bp
        0.8
        ES-0022b_2
        20.6%
        57%
        274 bp
        0.8
        ES-0022c_1
        15.8%
        57%
        259 bp
        0.6
        ES-0022c_2
        13.8%
        57%
        259 bp
        0.6
        ES-0023a_1
        17.7%
        56%
        272 bp
        0.6
        ES-0023a_2
        17.2%
        56%
        273 bp
        0.6
        ES-0023b_1
        11.7%
        56%
        269 bp
        0.2
        ES-0023b_2
        10.9%
        56%
        270 bp
        0.2
        ES-0023c_1
        10.7%
        57%
        256 bp
        0.4
        ES-0023c_2
        9.0%
        57%
        257 bp
        0.4
        ES-0024a_1
        11.5%
        56%
        274 bp
        0.3
        ES-0024a_2
        11.2%
        57%
        275 bp
        0.3
        ES-0024b_1
        6.2%
        57%
        283 bp
        0.1
        ES-0024b_2
        5.7%
        57%
        284 bp
        0.1
        ES-0024c_1
        21.3%
        57%
        275 bp
        0.8
        ES-0024c_2
        18.6%
        57%
        276 bp
        0.8
        ES-0025a_1
        15.5%
        56%
        254 bp
        0.5
        ES-0025a_2
        15.0%
        56%
        254 bp
        0.5
        ES-0025b_1
        15.0%
        56%
        280 bp
        0.5
        ES-0025b_2
        14.4%
        57%
        281 bp
        0.5
        ES-0025c_1
        18.9%
        57%
        274 bp
        0.6
        ES-0025c_2
        14.0%
        59%
        280 bp
        0.6
        ES-0026a_1
        12.4%
        56%
        272 bp
        0.4
        ES-0026a_2
        11.8%
        56%
        273 bp
        0.4
        ES-0026b_1
        12.3%
        56%
        258 bp
        0.4
        ES-0026b_2
        11.9%
        57%
        259 bp
        0.4
        ES-0026c_1
        22.6%
        57%
        271 bp
        0.9
        ES-0026c_2
        20.5%
        57%
        271 bp
        0.9
        ES-0027b_1
        12.9%
        56%
        283 bp
        0.3
        ES-0027b_2
        12.0%
        57%
        284 bp
        0.3
        ES-0027c_1
        33.5%
        57%
        238 bp
        1.5
        ES-0027c_2
        32.8%
        57%
        240 bp
        1.5
        ES-0028a_1
        16.2%
        56%
        262 bp
        0.5
        ES-0028a_2
        15.8%
        56%
        263 bp
        0.5
        ES-0028b_1
        13.3%
        56%
        272 bp
        0.4
        ES-0028b_2
        12.5%
        57%
        273 bp
        0.4
        ES-0028c_1
        17.0%
        57%
        273 bp
        0.6
        ES-0028c_2
        12.4%
        59%
        278 bp
        0.6
        ES-0132a_1
        16.8%
        57%
        261 bp
        0.6
        ES-0132a_2
        16.2%
        57%
        265 bp
        0.6
        ES-0132b_1
        21.3%
        57%
        277 bp
        0.8
        ES-0132b_2
        19.3%
        58%
        278 bp
        0.8
        ES-0133a_1
        19.8%
        57%
        282 bp
        0.7
        ES-0133a_2
        17.7%
        58%
        283 bp
        0.7
        ES-0133b_1
        25.2%
        57%
        273 bp
        0.8
        ES-0133b_2
        22.8%
        57%
        275 bp
        0.8
        ES-0133c_1
        12.4%
        57%
        283 bp
        0.4
        ES-0133c_2
        10.7%
        58%
        284 bp
        0.4

        Kraken Genus Map Report

        Kraken Genus Map Report kraken-mpa-report --db $minikrakenDB mini_kraken/*sequences.kraken >mini_kraken/mpa_report.tsv

        loading..

        Kraken Species Map Report

        Kraken Species Map Report kraken-mpa-report --db /group/ag_abi/kneubert/soft/Kraken/krakenDB/minikraken_20171019_8GB mini_kraken/*sequences.kraken >mini_kraken/mpa_report.tsv

        loading..

        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.

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


        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.

        176 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.

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