Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        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

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.7

        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 2020-07-08, 13:43 based on data in:

        General Statistics

        Showing 126/126 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        fastqc | MantonBM1_HiSeq_1_S1_L007_R2_001
        63.6%
        47%
        50.2
        fastqc | MantonBM1_HiSeq_1_S1_L008_R2_001
        63.6%
        47%
        48.5
        fastqc | MantonBM1_HiSeq_2_S2_L007_R2_001
        62.7%
        48%
        49.7
        fastqc | MantonBM1_HiSeq_2_S2_L008_R2_001
        62.8%
        48%
        47.4
        fastqc | MantonBM1_HiSeq_3_S3_L007_R2_001
        61.7%
        48%
        49.2
        fastqc | MantonBM1_HiSeq_3_S3_L008_R2_001
        61.7%
        48%
        46.7
        fastqc | MantonBM1_HiSeq_4_S4_L007_R2_001
        62.4%
        48%
        53.3
        fastqc | MantonBM1_HiSeq_4_S4_L008_R2_001
        62.3%
        48%
        50.9
        fastqc | MantonBM1_HiSeq_5_S5_L007_R2_001
        63.8%
        47%
        58.3
        fastqc | MantonBM1_HiSeq_5_S5_L008_R2_001
        63.7%
        47%
        56.0
        fastqc | MantonBM1_HiSeq_6_S6_L007_R2_001
        65.3%
        47%
        62.4
        fastqc | MantonBM1_HiSeq_6_S6_L008_R2_001
        65.3%
        47%
        60.2
        fastqc | MantonBM1_HiSeq_7_S7_L007_R2_001
        64.8%
        48%
        60.2
        fastqc | MantonBM1_HiSeq_7_S7_L008_R2_001
        65.1%
        47%
        58.0
        fastqc | MantonBM1_HiSeq_8_S8_L007_R2_001
        65.0%
        48%
        59.6
        fastqc | MantonBM1_HiSeq_8_S8_L008_R2_001
        65.0%
        47%
        57.5
        fastqc | MantonBM2_HiSeq_1_S9_L005_R2_001
        65.4%
        48%
        51.1
        fastqc | MantonBM2_HiSeq_1_S9_L006_R2_001
        63.5%
        48%
        46.9
        fastqc | MantonBM2_HiSeq_2_S10_L005_R2_001
        66.8%
        48%
        58.0
        fastqc | MantonBM2_HiSeq_2_S10_L006_R2_001
        64.8%
        47%
        53.0
        fastqc | MantonBM2_HiSeq_3_S11_L005_R2_001
        65.7%
        47%
        56.0
        fastqc | MantonBM2_HiSeq_3_S11_L006_R2_001
        64.0%
        47%
        51.3
        fastqc | MantonBM2_HiSeq_4_S12_L005_R2_001
        65.6%
        48%
        54.3
        fastqc | MantonBM2_HiSeq_4_S12_L006_R2_001
        64.3%
        47%
        50.0
        fastqc | MantonBM2_HiSeq_5_S13_L005_R2_001
        67.6%
        48%
        59.6
        fastqc | MantonBM2_HiSeq_5_S13_L006_R2_001
        65.9%
        48%
        54.8
        fastqc | MantonBM2_HiSeq_6_S14_L005_R2_001
        67.3%
        48%
        59.5
        fastqc | MantonBM2_HiSeq_6_S14_L006_R2_001
        65.5%
        48%
        54.8
        fastqc | MantonBM2_HiSeq_7_S15_L005_R2_001
        68.8%
        48%
        67.9
        fastqc | MantonBM2_HiSeq_7_S15_L006_R2_001
        66.9%
        48%
        62.4
        fastqc | MantonBM2_HiSeq_8_S16_L005_R2_001
        67.2%
        48%
        54.1
        fastqc | MantonBM2_HiSeq_8_S16_L006_R2_001
        65.3%
        48%
        49.8
        fastqc | MantonBM3_HiSeq_1_S17_L003_R2_001
        65.6%
        47%
        55.0
        fastqc | MantonBM3_HiSeq_1_S17_L004_R2_001
        65.0%
        47%
        52.0
        fastqc | MantonBM3_HiSeq_2_S18_L003_R2_001
        67.5%
        47%
        77.5
        fastqc | MantonBM3_HiSeq_2_S18_L004_R2_001
        66.9%
        47%
        72.5
        fastqc | MantonBM3_HiSeq_3_S19_L003_R2_001
        65.3%
        47%
        55.0
        fastqc | MantonBM3_HiSeq_3_S19_L004_R2_001
        64.8%
        47%
        51.6
        fastqc | MantonBM3_HiSeq_4_S20_L003_R2_001
        67.1%
        47%
        69.0
        fastqc | MantonBM3_HiSeq_4_S20_L004_R2_001
        66.5%
        47%
        65.1
        fastqc | MantonBM3_HiSeq_5_S21_L003_R2_001
        65.4%
        47%
        53.1
        fastqc | MantonBM3_HiSeq_5_S21_L004_R2_001
        64.5%
        47%
        49.6
        fastqc | MantonBM3_HiSeq_6_S22_L003_R2_001
        65.6%
        47%
        54.5
        fastqc | MantonBM3_HiSeq_6_S22_L004_R2_001
        64.6%
        47%
        50.9
        fastqc | MantonBM3_HiSeq_7_S23_L003_R2_001
        63.8%
        47%
        49.3
        fastqc | MantonBM3_HiSeq_7_S23_L004_R2_001
        62.8%
        47%
        45.7
        fastqc | MantonBM3_HiSeq_8_S24_L003_R2_001
        65.9%
        47%
        53.0
        fastqc | MantonBM3_HiSeq_8_S24_L004_R2_001
        65.5%
        47%
        50.0
        fastqc | MantonBM4_HiSeq_1_S25_L001_R2_001
        68.4%
        47%
        61.6
        fastqc | MantonBM4_HiSeq_1_S25_L002_R2_001
        68.0%
        47%
        60.5
        fastqc | MantonBM4_HiSeq_2_S26_L001_R2_001
        66.7%
        48%
        52.6
        fastqc | MantonBM4_HiSeq_2_S26_L002_R2_001
        66.0%
        47%
        49.3
        fastqc | MantonBM4_HiSeq_3_S27_L001_R2_001
        67.5%
        48%
        54.6
        fastqc | MantonBM4_HiSeq_3_S27_L002_R2_001
        67.1%
        47%
        52.7
        fastqc | MantonBM4_HiSeq_4_S28_L001_R2_001
        67.3%
        47%
        56.0
        fastqc | MantonBM4_HiSeq_4_S28_L002_R2_001
        67.1%
        47%
        54.3
        fastqc | MantonBM4_HiSeq_5_S29_L001_R2_001
        67.8%
        48%
        59.1
        fastqc | MantonBM4_HiSeq_5_S29_L002_R2_001
        67.1%
        47%
        55.7
        fastqc | MantonBM4_HiSeq_6_S30_L001_R2_001
        67.1%
        48%
        55.2
        fastqc | MantonBM4_HiSeq_6_S30_L002_R2_001
        66.5%
        47%
        52.3
        fastqc | MantonBM4_HiSeq_7_S31_L001_R2_001
        67.1%
        47%
        54.6
        fastqc | MantonBM4_HiSeq_7_S31_L002_R2_001
        66.0%
        47%
        51.9
        fastqc | MantonBM4_HiSeq_8_S32_L001_R2_001
        69.2%
        47%
        61.1
        fastqc | MantonBM4_HiSeq_8_S32_L002_R2_001
        69.0%
        47%
        60.9
        fastqc | MantonBM5_HiSeq_1_S1_L001_R2_001
        68.8%
        48%
        60.8
        fastqc | MantonBM5_HiSeq_1_S1_L002_R2_001
        69.9%
        48%
        62.0
        fastqc | MantonBM5_HiSeq_2_S2_L001_R2_001
        69.2%
        48%
        62.5
        fastqc | MantonBM5_HiSeq_2_S2_L002_R2_001
        70.0%
        48%
        63.7
        fastqc | MantonBM5_HiSeq_3_S3_L001_R2_001
        69.1%
        48%
        63.8
        fastqc | MantonBM5_HiSeq_3_S3_L002_R2_001
        70.0%
        48%
        65.0
        fastqc | MantonBM5_HiSeq_4_S4_L001_R2_001
        69.1%
        48%
        61.1
        fastqc | MantonBM5_HiSeq_4_S4_L002_R2_001
        70.1%
        48%
        62.2
        fastqc | MantonBM5_HiSeq_5_S5_L001_R2_001
        68.8%
        48%
        62.7
        fastqc | MantonBM5_HiSeq_5_S5_L002_R2_001
        69.7%
        48%
        64.0
        fastqc | MantonBM5_HiSeq_6_S6_L001_R2_001
        68.7%
        48%
        60.9
        fastqc | MantonBM5_HiSeq_6_S6_L002_R2_001
        70.0%
        48%
        62.1
        fastqc | MantonBM5_HiSeq_7_S7_L001_R2_001
        68.9%
        47%
        47.1
        fastqc | MantonBM5_HiSeq_7_S7_L002_R2_001
        69.9%
        47%
        47.8
        fastqc | MantonBM5_HiSeq_8_S8_L001_R2_001
        69.0%
        48%
        55.7
        fastqc | MantonBM5_HiSeq_8_S8_L002_R2_001
        69.7%
        48%
        56.7
        fastqc | MantonBM6_HiSeq_1_S9_L003_R2_001
        67.4%
        47%
        66.7
        fastqc | MantonBM6_HiSeq_1_S9_L004_R2_001
        66.4%
        47%
        67.0
        fastqc | MantonBM6_HiSeq_2_S10_L003_R2_001
        68.7%
        47%
        70.4
        fastqc | MantonBM6_HiSeq_2_S10_L004_R2_001
        68.6%
        47%
        70.8
        fastqc | MantonBM6_HiSeq_4_S11_L003_R2_001
        69.2%
        47%
        67.8
        fastqc | MantonBM6_HiSeq_4_S11_L004_R2_001
        68.1%
        47%
        68.0
        fastqc | MantonBM6_HiSeq_5_S12_L003_R2_001
        68.0%
        47%
        67.2
        fastqc | MantonBM6_HiSeq_5_S12_L004_R2_001
        68.6%
        47%
        67.6
        fastqc | MantonBM6_HiSeq_6_S13_L003_R2_001
        69.5%
        47%
        74.3
        fastqc | MantonBM6_HiSeq_6_S13_L004_R2_001
        69.6%
        47%
        74.7
        fastqc | MantonBM6_HiSeq_7_S14_L003_R2_001
        68.5%
        47%
        66.7
        fastqc | MantonBM6_HiSeq_7_S14_L004_R2_001
        67.7%
        47%
        67.0
        fastqc | MantonBM6_HiSeq_8_S15_L003_R2_001
        68.9%
        47%
        70.3
        fastqc | MantonBM6_HiSeq_8_S15_L004_R2_001
        69.2%
        47%
        70.7
        fastqc | MantonBM7_HiSeq_1_S16_L005_R2_001
        64.4%
        47%
        38.6
        fastqc | MantonBM7_HiSeq_1_S16_L006_R2_001
        66.0%
        47%
        45.9
        fastqc | MantonBM7_HiSeq_2_S17_L005_R2_001
        65.5%
        47%
        43.1
        fastqc | MantonBM7_HiSeq_2_S17_L006_R2_001
        66.8%
        47%
        51.4
        fastqc | MantonBM7_HiSeq_3_S18_L005_R2_001
        65.3%
        47%
        43.7
        fastqc | MantonBM7_HiSeq_3_S18_L006_R2_001
        66.5%
        47%
        51.8
        fastqc | MantonBM7_HiSeq_4_S19_L005_R2_001
        66.8%
        47%
        52.6
        fastqc | MantonBM7_HiSeq_4_S19_L006_R2_001
        68.2%
        47%
        62.1
        fastqc | MantonBM7_HiSeq_5_S20_L005_R2_001
        65.4%
        47%
        40.0
        fastqc | MantonBM7_HiSeq_5_S20_L006_R2_001
        66.9%
        47%
        47.5
        fastqc | MantonBM7_HiSeq_6_S21_L005_R2_001
        64.1%
        47%
        38.5
        fastqc | MantonBM7_HiSeq_6_S21_L006_R2_001
        65.5%
        47%
        46.1
        fastqc | MantonBM7_HiSeq_7_S22_L005_R2_001
        64.6%
        47%
        36.0
        fastqc | MantonBM7_HiSeq_7_S22_L006_R2_001
        66.3%
        47%
        43.0
        fastqc | MantonBM7_HiSeq_8_S23_L005_R2_001
        65.9%
        47%
        41.4
        fastqc | MantonBM7_HiSeq_8_S23_L006_R2_001
        67.2%
        47%
        49.2
        fastqc | MantonBM8_HiSeq_1_S24_L007_R2_001
        69.9%
        47%
        54.6
        fastqc | MantonBM8_HiSeq_1_S24_L008_R2_001
        69.4%
        47%
        51.5
        fastqc | MantonBM8_HiSeq_2_S25_L007_R2_001
        69.4%
        47%
        49.4
        fastqc | MantonBM8_HiSeq_2_S25_L008_R2_001
        69.2%
        47%
        46.5
        fastqc | MantonBM8_HiSeq_3_S26_L007_R2_001
        69.9%
        47%
        49.1
        fastqc | MantonBM8_HiSeq_3_S26_L008_R2_001
        69.6%
        47%
        46.2
        fastqc | MantonBM8_HiSeq_4_S27_L007_R2_001
        70.9%
        47%
        53.7
        fastqc | MantonBM8_HiSeq_4_S27_L008_R2_001
        70.9%
        47%
        50.8
        fastqc | MantonBM8_HiSeq_5_S28_L007_R2_001
        69.6%
        47%
        50.4
        fastqc | MantonBM8_HiSeq_5_S28_L008_R2_001
        69.4%
        47%
        47.5
        fastqc | MantonBM8_HiSeq_6_S29_L007_R2_001
        70.0%
        47%
        51.7
        fastqc | MantonBM8_HiSeq_6_S29_L008_R2_001
        69.8%
        47%
        48.8
        fastqc | MantonBM8_HiSeq_7_S30_L007_R2_001
        69.5%
        47%
        49.8
        fastqc | MantonBM8_HiSeq_7_S30_L008_R2_001
        69.5%
        47%
        47.0
        fastqc | MantonBM8_HiSeq_8_S31_L007_R2_001
        70.2%
        48%
        45.2
        fastqc | MantonBM8_HiSeq_8_S31_L008_R2_001
        69.8%
        48%
        42.6

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

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

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        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.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        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.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        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.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        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.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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

        Sequence Length Distribution

        All samples have sequences of a single length (98bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        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.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

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

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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

        MultiQC v1.7 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.