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        Note that additional data was saved in multiqc_PRJNA389927_report_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 1.15

        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 2023-09-14, 14:25 PDT based on data in:

        General Statistics

        Showing 181/181 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SRR5665009
        43.6%
        44%
        251 bp
        0.8
        SRR5665010
        67.6%
        41%
        251 bp
        1.9
        SRR5665011
        56.1%
        42%
        251 bp
        2.5
        SRR5665012
        77.9%
        43%
        251 bp
        2.2
        SRR5665013
        33.4%
        46%
        251 bp
        3.7
        SRR5665014
        74.0%
        48%
        251 bp
        4.7
        SRR5665015
        80.4%
        39%
        251 bp
        2.3
        SRR5665016
        79.9%
        50%
        251 bp
        1.9
        SRR5665017
        86.8%
        39%
        251 bp
        3.9
        SRR5665018
        64.1%
        42%
        251 bp
        1.7
        SRR5665019
        61.7%
        45%
        251 bp
        1.9
        SRR5665020
        53.3%
        47%
        251 bp
        4.3
        SRR5665021
        69.7%
        47%
        251 bp
        1.4
        SRR5665022
        79.4%
        37%
        251 bp
        3.9
        SRR5665023
        63.5%
        39%
        251 bp
        1.5
        SRR5665024
        4.4%
        45%
        251 bp
        0.0
        SRR5665025
        3.6%
        48%
        251 bp
        2.4
        SRR5665026
        4.4%
        48%
        250 bp
        1.6
        SRR5665027
        9.9%
        48%
        251 bp
        3.9
        SRR5665028
        6.8%
        46%
        251 bp
        3.5
        SRR5665029
        7.3%
        47%
        251 bp
        3.2
        SRR5665030
        16.6%
        48%
        251 bp
        4.8
        SRR5665031
        19.8%
        45%
        251 bp
        4.9
        SRR5665032
        8.3%
        46%
        251 bp
        1.7
        SRR5665033
        8.8%
        46%
        251 bp
        2.4
        SRR5665034
        8.3%
        48%
        251 bp
        2.5
        SRR5665035
        7.3%
        46%
        251 bp
        2.5
        SRR5665036
        12.4%
        56%
        251 bp
        0.2
        SRR5665037
        72.1%
        38%
        251 bp
        2.0
        SRR5665038
        62.2%
        44%
        250 bp
        5.2
        SRR5665039
        75.3%
        42%
        251 bp
        4.4
        SRR5665040
        66.6%
        46%
        251 bp
        6.7
        SRR5665041
        13.1%
        46%
        251 bp
        3.9
        SRR5665042
        15.4%
        50%
        251 bp
        2.7
        SRR5665043
        8.6%
        47%
        251 bp
        5.1
        SRR5665044
        10.7%
        46%
        251 bp
        3.5
        SRR5665045
        1.0%
        46%
        250 bp
        0.2
        SRR5665046
        8.2%
        48%
        251 bp
        5.2
        SRR5665047
        8.3%
        49%
        251 bp
        3.1
        SRR5665048
        7.1%
        45%
        251 bp
        2.6
        SRR5665049
        14.3%
        44%
        251 bp
        4.6
        SRR5665050
        9.3%
        47%
        251 bp
        3.6
        SRR5665051
        5.5%
        50%
        250 bp
        2.1
        SRR5665052
        8.6%
        49%
        251 bp
        3.6
        SRR5665053
        8.2%
        47%
        251 bp
        3.0
        SRR5665054
        12.5%
        50%
        251 bp
        4.9
        SRR5665055
        16.2%
        51%
        251 bp
        7.4
        SRR5665056
        2.5%
        48%
        250 bp
        0.7
        SRR5665057
        5.4%
        50%
        251 bp
        2.5
        SRR5665058
        5.9%
        49%
        251 bp
        2.2
        SRR5665059
        14.0%
        45%
        251 bp
        3.4
        SRR5665060
        3.7%
        45%
        242 bp
        0.0
        SRR5665061
        7.9%
        46%
        251 bp
        3.1
        SRR5665062
        52.1%
        50%
        251 bp
        4.5
        SRR5665063
        65.3%
        43%
        251 bp
        3.1
        SRR5665064
        62.0%
        47%
        251 bp
        7.9
        SRR5665065
        67.6%
        45%
        251 bp
        3.2
        SRR5665066
        77.0%
        40%
        251 bp
        2.2
        SRR5665067
        74.2%
        45%
        251 bp
        3.1
        SRR5665068
        66.2%
        37%
        251 bp
        1.1
        SRR5665069
        41.1%
        45%
        251 bp
        0.5
        SRR5665070
        73.3%
        45%
        250 bp
        0.4
        SRR5665071
        55.0%
        46%
        251 bp
        3.5
        SRR5665072
        9.1%
        47%
        251 bp
        7.6
        SRR5665073
        22.5%
        50%
        251 bp
        6.3
        SRR5665074
        5.5%
        49%
        251 bp
        3.2
        SRR5665075
        14.0%
        47%
        251 bp
        4.7
        SRR5665076
        3.8%
        45%
        251 bp
        1.3
        SRR5665077
        8.7%
        47%
        251 bp
        3.7
        SRR5665078
        7.1%
        50%
        251 bp
        2.8
        SRR5665079
        7.4%
        49%
        251 bp
        4.1
        SRR5665080
        12.5%
        47%
        250 bp
        2.7
        SRR5665081
        9.7%
        49%
        251 bp
        0.0
        SRR5665082
        81.6%
        42%
        251 bp
        3.8
        SRR5665083
        67.4%
        52%
        251 bp
        2.9
        SRR5665084
        64.6%
        47%
        251 bp
        3.2
        SRR5665085
        15.6%
        44%
        251 bp
        3.1
        SRR5665086
        17.0%
        41%
        251 bp
        0.2
        SRR5665087
        72.3%
        45%
        251 bp
        3.2
        SRR5665088
        64.6%
        38%
        251 bp
        1.4
        SRR5665089
        61.6%
        40%
        251 bp
        0.4
        SRR5665090
        62.7%
        45%
        251 bp
        2.5
        SRR5665091
        79.7%
        47%
        251 bp
        5.1
        SRR5665092
        82.0%
        49%
        251 bp
        4.0
        SRR5665093
        15.3%
        61%
        250 bp
        2.8
        SRR5665094
        16.1%
        55%
        251 bp
        0.2
        SRR5665095
        4.8%
        55%
        251 bp
        0.1
        SRR5665096
        0.1%
        53%
        242 bp
        0.0
        SRR5665097
        13.2%
        54%
        251 bp
        0.3
        SRR5665098
        10.3%
        54%
        251 bp
        0.1
        SRR5665099
        13.8%
        58%
        251 bp
        0.8
        SRR5665100
        8.2%
        56%
        251 bp
        0.2
        SRR5665101
        10.2%
        58%
        251 bp
        0.9
        SRR5665102
        14.8%
        55%
        251 bp
        0.2
        SRR5665103
        11.7%
        46%
        251 bp
        3.4
        SRR5665104
        27.9%
        47%
        251 bp
        0.1
        SRR5665105
        29.3%
        53%
        251 bp
        0.5
        SRR5665106
        62.2%
        43%
        251 bp
        7.0
        SRR5665107
        9.1%
        44%
        251 bp
        0.4
        SRR5665108
        84.7%
        39%
        251 bp
        14.4
        SRR5665109
        61.7%
        47%
        251 bp
        1.9
        SRR5665110
        58.0%
        43%
        251 bp
        5.3
        SRR5665111
        59.2%
        46%
        251 bp
        1.6
        SRR5665112
        54.2%
        43%
        251 bp
        2.8
        SRR5665113
        30.2%
        45%
        251 bp
        0.2
        SRR5665114
        4.1%
        46%
        251 bp
        1.0
        SRR5665115
        5.1%
        46%
        251 bp
        1.4
        SRR5665116
        6.1%
        46%
        251 bp
        1.2
        SRR5665117
        0.2%
        49%
        251 bp
        0.0
        SRR5665118
        9.7%
        46%
        251 bp
        2.5
        SRR5665119
        1.8%
        48%
        251 bp
        1.3
        SRR5665120
        14.2%
        48%
        251 bp
        6.1
        SRR5665121
        7.2%
        51%
        242 bp
        0.0
        SRR5665122
        18.6%
        47%
        251 bp
        10.7
        SRR5665123
        11.4%
        51%
        251 bp
        5.1
        SRR5665124
        64.9%
        41%
        251 bp
        2.0
        SRR5665125
        62.9%
        42%
        251 bp
        4.0
        SRR5665126
        76.6%
        50%
        251 bp
        2.4
        SRR5665127
        87.7%
        48%
        251 bp
        2.7
        SRR5665128
        62.8%
        40%
        251 bp
        1.8
        SRR5665129
        71.3%
        41%
        251 bp
        2.7
        SRR5665130
        64.5%
        43%
        251 bp
        2.1
        SRR5665131
        10.7%
        45%
        251 bp
        1.8
        SRR5665132
        48.1%
        47%
        250 bp
        2.7
        SRR5665133
        33.5%
        45%
        251 bp
        0.4
        SRR5665134
        7.5%
        46%
        251 bp
        2.1
        SRR5665135
        5.7%
        49%
        251 bp
        2.1
        SRR5665136
        8.3%
        49%
        251 bp
        2.6
        SRR5665137
        19.5%
        50%
        251 bp
        2.2
        SRR5665138
        4.8%
        46%
        247 bp
        0.0
        SRR5665139
        8.4%
        47%
        251 bp
        1.9
        SRR5665140
        6.5%
        45%
        251 bp
        2.1
        SRR5665141
        6.3%
        44%
        251 bp
        1.3
        SRR5665142
        7.1%
        49%
        251 bp
        2.0
        SRR5665143
        4.8%
        48%
        251 bp
        2.2
        SRR5665144
        6.1%
        46%
        251 bp
        2.6
        SRR5665145
        44.0%
        44%
        247 bp
        0.0
        SRR5665146
        69.5%
        40%
        251 bp
        1.9
        SRR5665147
        46.1%
        48%
        251 bp
        2.4
        SRR5665148
        65.4%
        44%
        251 bp
        1.9
        SRR5665149
        57.9%
        44%
        251 bp
        2.5
        SRR5665150
        60.7%
        45%
        251 bp
        6.0
        SRR5665151
        44.2%
        44%
        251 bp
        1.6
        SRR5665152
        26.4%
        45%
        251 bp
        0.1
        SRR5665153
        77.7%
        42%
        251 bp
        5.2
        SRR5665154
        65.4%
        41%
        251 bp
        3.2
        SRR5665155
        20.2%
        48%
        251 bp
        3.8
        SRR5665156
        3.0%
        50%
        251 bp
        1.5
        SRR5665157
        4.6%
        47%
        251 bp
        1.5
        SRR5665158
        6.1%
        48%
        251 bp
        2.9
        SRR5665159
        5.5%
        49%
        251 bp
        1.2
        SRR5665160
        12.1%
        46%
        251 bp
        0.2
        SRR5665161
        9.8%
        50%
        251 bp
        1.3
        SRR5665162
        16.9%
        47%
        251 bp
        5.9
        SRR5665163
        3.9%
        49%
        250 bp
        1.5
        SRR5665164
        5.6%
        49%
        251 bp
        3.0
        SRR5665165
        1.1%
        42%
        251 bp
        0.0
        SRR5665166
        52.8%
        35%
        251 bp
        0.2
        SRR5665167
        36.2%
        42%
        251 bp
        1.9
        SRR5665168
        78.3%
        40%
        251 bp
        5.0
        SRR5665169
        3.1%
        44%
        247 bp
        0.0
        SRR5665170
        69.2%
        42%
        251 bp
        6.7
        SRR5665171
        7.0%
        51%
        251 bp
        0.0
        SRR5665172
        26.6%
        47%
        251 bp
        0.1
        SRR5665173
        52.1%
        43%
        251 bp
        1.5
        SRR5665174
        51.6%
        42%
        251 bp
        3.3
        SRR5665175
        39.1%
        47%
        251 bp
        0.6
        SRR5665176
        0.0%
        0%
        0 bp
        0.0
        SRR5665177
        52.6%
        45%
        250 bp
        1.2
        SRR5665178
        7.0%
        46%
        251 bp
        2.0
        SRR5665179
        6.3%
        46%
        251 bp
        2.9
        SRR5665180
        1.7%
        47%
        250 bp
        0.2
        SRR5665181
        12.0%
        51%
        251 bp
        3.9
        SRR5665182
        14.7%
        46%
        251 bp
        6.0
        SRR5665183
        10.3%
        45%
        251 bp
        2.7
        SRR5665184
        12.5%
        47%
        251 bp
        4.7
        SRR5665185
        5.6%
        48%
        251 bp
        3.0
        SRR5665186
        8.3%
        46%
        251 bp
        5.5
        SRR5665187
        13.7%
        49%
        251 bp
        9.1
        SRR5665188
        80.5%
        38%
        251 bp
        3.0
        SRR5665189
        57.9%
        52%
        251 bp
        0.6

        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.

        loading..

        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.

        loading..

        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.

        loading..

        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.

        loading..

        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.

        loading..

        Sequence Length Distribution

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

        loading..

        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.

        loading..

        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.

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        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.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.15 - Written by Phil Ewels, available on GitHub.

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