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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, 14:26 PDT based on data in:


        General Statistics

        Showing 223/223 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SRR15647901
        16.8%
        45%
        200 bp
        25.9
        SRR15647902
        21.6%
        47%
        200 bp
        24.4
        SRR15647903
        50.9%
        46%
        200 bp
        20.6
        SRR15647904
        39.9%
        45%
        200 bp
        20.9
        SRR15647905
        20.7%
        45%
        200 bp
        16.9
        SRR15647906
        0.0%
        0%
        0 bp
        0.0
        SRR15647907
        0.0%
        0%
        0 bp
        0.0
        SRR15647908
        5.5%
        49%
        200 bp
        1.1
        SRR15647909
        8.7%
        48%
        200 bp
        5.5
        SRR15647910
        32.4%
        46%
        200 bp
        20.9
        SRR15647911
        21.2%
        46%
        200 bp
        18.2
        SRR15647912
        16.5%
        49%
        200 bp
        24.2
        SRR15647913
        2.7%
        46%
        200 bp
        0.8
        SRR15647914
        8.7%
        44%
        200 bp
        1.8
        SRR15647915
        24.0%
        47%
        200 bp
        7.9
        SRR15647916
        23.7%
        47%
        200 bp
        24.9
        SRR15647917
        4.6%
        45%
        200 bp
        0.6
        SRR15647918
        17.3%
        47%
        200 bp
        36.6
        SRR15647919
        28.1%
        44%
        200 bp
        48.7
        SRR15647920
        13.6%
        49%
        200 bp
        35.3
        SRR15647921
        22.0%
        48%
        200 bp
        31.6
        SRR15647922
        13.2%
        45%
        200 bp
        17.5
        SRR15647923
        11.0%
        47%
        200 bp
        22.0
        SRR15647924
        24.3%
        46%
        200 bp
        28.8
        SRR15647925
        0.0%
        0%
        0 bp
        0.0
        SRR15647926
        3.1%
        49%
        200 bp
        1.6
        SRR15647927
        13.6%
        44%
        200 bp
        15.8
        SRR15647928
        11.7%
        49%
        200 bp
        21.2
        SRR15647929
        5.3%
        45%
        200 bp
        2.8
        SRR15647930
        13.1%
        49%
        200 bp
        18.6
        SRR15647931
        15.5%
        47%
        200 bp
        21.1
        SRR15647932
        28.8%
        44%
        200 bp
        31.4
        SRR15647933
        26.3%
        45%
        200 bp
        29.8
        SRR15647934
        44.4%
        45%
        200 bp
        29.6
        SRR15647935
        0.0%
        0%
        0 bp
        0.0
        SRR15647936
        25.3%
        44%
        200 bp
        39.8
        SRR15647937
        12.6%
        47%
        200 bp
        25.3
        SRR15647938
        0.0%
        0%
        0 bp
        0.0
        SRR15647939
        0.0%
        0%
        0 bp
        0.0
        SRR15647940
        18.5%
        45%
        200 bp
        18.6
        SRR15647941
        0.0%
        0%
        0 bp
        0.0
        SRR15647942
        20.5%
        48%
        200 bp
        7.0
        SRR15647943
        19.7%
        47%
        200 bp
        20.4
        SRR15647944
        37.9%
        44%
        200 bp
        26.1
        SRR15647945
        6.9%
        47%
        200 bp
        3.0
        SRR15647946
        0.0%
        0%
        0 bp
        0.0
        SRR15647947
        15.7%
        46%
        200 bp
        21.8
        SRR15647948
        33.4%
        47%
        200 bp
        33.5
        SRR15647949
        0.0%
        0%
        0 bp
        0.0
        SRR15647950
        0.0%
        0%
        0 bp
        0.0
        SRR15647951
        0.0%
        0%
        0 bp
        0.0
        SRR15647952
        25.9%
        44%
        200 bp
        21.2
        SRR15647953
        21.6%
        47%
        200 bp
        33.6
        SRR15647954
        0.0%
        0%
        0 bp
        0.0
        SRR15647955
        2.8%
        46%
        200 bp
        0.9
        SRR15647956
        24.6%
        47%
        200 bp
        41.6
        SRR15647957
        0.0%
        0%
        0 bp
        0.0
        SRR15647958
        0.0%
        0%
        0 bp
        0.0
        SRR15647959
        0.0%
        0%
        0 bp
        0.0
        SRR15647960
        14.4%
        48%
        200 bp
        41.4
        SRR15647961
        24.0%
        47%
        200 bp
        29.9
        SRR15647962
        8.8%
        48%
        200 bp
        9.3
        SRR15647963
        29.4%
        47%
        200 bp
        23.8
        SRR15647964
        10.4%
        51%
        200 bp
        26.2
        SRR15647965
        0.0%
        0%
        0 bp
        0.0
        SRR15647966
        3.2%
        46%
        200 bp
        0.9
        SRR15647967
        4.7%
        47%
        200 bp
        2.0
        SRR15647968
        17.8%
        45%
        200 bp
        22.5
        SRR15647969
        17.6%
        46%
        200 bp
        19.6
        SRR15647970
        0.0%
        0%
        0 bp
        0.0
        SRR15647971
        6.0%
        46%
        200 bp
        1.9
        SRR15647972
        12.5%
        50%
        200 bp
        23.9
        SRR15647973
        7.3%
        45%
        200 bp
        8.5
        SRR15647974
        10.3%
        45%
        200 bp
        3.1
        SRR15647975
        15.6%
        46%
        200 bp
        25.0
        SRR15647976
        8.1%
        45%
        200 bp
        6.7
        SRR15647977
        0.0%
        0%
        0 bp
        0.0
        SRR15647978
        4.8%
        45%
        200 bp
        0.5
        SRR15647979
        16.3%
        47%
        200 bp
        19.3
        SRR15647980
        14.9%
        45%
        200 bp
        17.5
        SRR15647981
        0.0%
        0%
        0 bp
        0.0
        SRR15647982
        28.9%
        46%
        200 bp
        17.8
        SRR15647983
        29.5%
        47%
        200 bp
        24.1
        SRR15647984
        10.4%
        46%
        200 bp
        9.1
        SRR15647985
        15.6%
        48%
        200 bp
        18.4
        SRR15647986
        14.8%
        46%
        200 bp
        19.4
        SRR15647987
        15.5%
        47%
        200 bp
        12.1
        SRR15647988
        0.0%
        0%
        0 bp
        0.0
        SRR15647989
        0.0%
        0%
        0 bp
        0.0
        SRR15647990
        25.5%
        45%
        200 bp
        44.2
        SRR15647991
        16.2%
        47%
        200 bp
        28.9
        SRR15647992
        14.5%
        48%
        200 bp
        22.1
        SRR15647993
        16.2%
        45%
        200 bp
        11.5
        SRR15647994
        18.6%
        44%
        200 bp
        13.7
        SRR15647995
        10.5%
        47%
        200 bp
        7.3
        SRR15647996
        24.7%
        50%
        200 bp
        30.5
        SRR15647997
        16.5%
        49%
        200 bp
        23.4
        SRR15674129
        27.3%
        46%
        100 bp
        50.9
        SRR15674130
        14.5%
        45%
        100 bp
        46.1
        SRR15674131
        67.7%
        52%
        100 bp
        72.4
        SRR15674132
        24.1%
        45%
        100 bp
        61.7
        SRR15674133
        24.7%
        45%
        100 bp
        57.0
        SRR15674134
        0.0%
        0%
        0 bp
        0.0
        SRR15674135
        27.8%
        42%
        100 bp
        20.6
        SRR15674136
        0.0%
        0%
        0 bp
        0.0
        SRR15674137
        6.1%
        46%
        100 bp
        42.3
        SRR15674138
        34.3%
        43%
        100 bp
        46.9
        SRR15674139
        0.0%
        0%
        0 bp
        0.0
        SRR15674140
        22.2%
        46%
        100 bp
        29.6
        SRR15674141
        20.3%
        42%
        100 bp
        46.1
        SRR15674142
        32.2%
        43%
        100 bp
        64.1
        SRR15674143
        0.0%
        0%
        0 bp
        0.0
        SRR15674144
        13.2%
        44%
        100 bp
        15.5
        SRR15674145
        35.8%
        44%
        100 bp
        50.9
        SRR15674146
        0.0%
        0%
        0 bp
        0.0
        SRR15674147
        0.0%
        0%
        0 bp
        0.0
        SRR15674148
        0.0%
        0%
        0 bp
        0.0
        SRR15674149
        27.9%
        44%
        100 bp
        55.3
        SRR15674150
        41.3%
        44%
        100 bp
        42.4
        SRR15674151
        15.7%
        44%
        100 bp
        51.9
        SRR15674152
        27.1%
        44%
        100 bp
        27.0
        SRR15674153
        4.5%
        45%
        100 bp
        3.4
        SRR15674154
        27.4%
        45%
        100 bp
        62.5
        SRR15674155
        0.0%
        0%
        0 bp
        0.0
        SRR15674156
        26.0%
        48%
        100 bp
        65.2
        SRR15674157
        22.2%
        43%
        100 bp
        21.4
        SRR15674158
        13.8%
        45%
        100 bp
        71.9
        SRR15674159
        30.0%
        44%
        100 bp
        29.4
        SRR15674160
        9.5%
        44%
        100 bp
        14.6
        SRR15674161
        0.0%
        0%
        0 bp
        0.0
        SRR15674162
        4.5%
        47%
        100 bp
        8.8
        SRR15674163
        22.0%
        47%
        100 bp
        53.7
        SRR15674164
        14.5%
        45%
        100 bp
        7.6
        SRR15674165
        13.7%
        45%
        100 bp
        30.8
        SRR15674166
        20.9%
        45%
        100 bp
        48.6
        SRR15674167
        17.6%
        43%
        100 bp
        55.9
        SRR15674168
        22.9%
        46%
        100 bp
        62.7
        SRR15674169
        2.8%
        47%
        100 bp
        10.2
        SRR15674170
        41.9%
        45%
        100 bp
        33.3
        SRR15674171
        0.0%
        0%
        0 bp
        0.0
        SRR15674172
        1.7%
        46%
        100 bp
        1.4
        SRR15674173
        15.7%
        43%
        100 bp
        22.0
        SRR15674174
        0.0%
        0%
        0 bp
        0.0
        SRR15674175
        0.0%
        0%
        0 bp
        0.0
        SRR15674176
        18.0%
        46%
        100 bp
        61.0
        SRR15674177
        0.0%
        0%
        0 bp
        0.0
        SRR15674178
        28.6%
        44%
        100 bp
        44.8
        SRR15674179
        17.3%
        43%
        100 bp
        14.7
        SRR15674180
        0.0%
        0%
        0 bp
        0.0
        SRR15674181
        19.0%
        47%
        100 bp
        49.8
        SRR15674182
        0.0%
        0%
        0 bp
        0.0
        SRR15674183
        10.6%
        46%
        100 bp
        44.5
        SRR15674184
        6.8%
        48%
        100 bp
        40.1
        SRR15674185
        27.5%
        42%
        100 bp
        47.9
        SRR15674186
        10.6%
        44%
        100 bp
        46.3
        SRR15674187
        3.5%
        43%
        100 bp
        8.1
        SRR15674188
        6.6%
        49%
        100 bp
        16.4
        SRR15674189
        22.5%
        43%
        100 bp
        42.3
        SRR15674190
        36.1%
        44%
        100 bp
        36.0
        SRR15674191
        20.8%
        45%
        100 bp
        47.3
        SRR15674192
        11.3%
        43%
        100 bp
        15.9
        SRR15674193
        22.2%
        44%
        100 bp
        36.6
        SRR15674194
        4.8%
        44%
        100 bp
        7.6
        SRR15674195
        19.5%
        44%
        100 bp
        42.3
        SRR15674196
        21.9%
        45%
        100 bp
        51.2
        SRR15674197
        0.0%
        0%
        0 bp
        0.0
        SRR15674198
        13.6%
        44%
        100 bp
        41.8
        SRR15674199
        7.4%
        43%
        100 bp
        11.9
        SRR15674200
        14.7%
        45%
        100 bp
        42.3
        SRR15674201
        18.5%
        43%
        100 bp
        38.8
        SRR15674202
        28.6%
        43%
        100 bp
        56.5
        SRR15674203
        4.2%
        41%
        100 bp
        1.9
        SRR15674204
        16.2%
        43%
        100 bp
        13.3
        SRR15674205
        19.1%
        43%
        100 bp
        22.6
        SRR15674206
        0.0%
        0%
        0 bp
        0.0
        SRR15674207
        13.2%
        46%
        100 bp
        25.1
        SRR15674208
        0.0%
        0%
        0 bp
        0.0
        SRR15674209
        0.0%
        0%
        0 bp
        0.0
        SRR15674210
        0.0%
        0%
        0 bp
        0.0
        SRR15674211
        20.3%
        44%
        100 bp
        58.3
        SRR15674212
        17.0%
        43%
        100 bp
        10.7
        SRR15674213
        19.2%
        44%
        100 bp
        45.6
        SRR15674214
        15.8%
        44%
        100 bp
        57.8
        SRR15674215
        39.7%
        43%
        100 bp
        47.0
        SRR15674216
        54.4%
        45%
        100 bp
        51.7
        SRR15674217
        14.1%
        46%
        100 bp
        50.7
        SRR15674218
        15.5%
        44%
        100 bp
        42.1
        SRR15674219
        28.9%
        43%
        100 bp
        38.2
        SRR15674220
        9.4%
        45%
        100 bp
        37.9
        SRR15674221
        14.4%
        45%
        100 bp
        49.8
        SRR15674222
        1.4%
        44%
        100 bp
        1.4
        SRR15674223
        2.7%
        45%
        100 bp
        8.4
        SRR15674224
        0.7%
        43%
        100 bp
        0.7
        SRR15674225
        10.5%
        46%
        100 bp
        16.9
        SRR15674226
        18.2%
        47%
        100 bp
        53.6
        SRR15674227
        19.6%
        46%
        100 bp
        46.7
        SRR15674228
        12.4%
        46%
        100 bp
        35.6
        SRR15674229
        16.3%
        46%
        100 bp
        56.8
        SRR15674230
        16.2%
        44%
        100 bp
        44.5
        SRR15674231
        11.3%
        45%
        100 bp
        19.1
        SRR15674232
        25.0%
        46%
        100 bp
        13.9
        SRR15674233
        4.7%
        46%
        100 bp
        3.9
        SRR15674234
        22.9%
        45%
        100 bp
        54.8
        SRR15674235
        1.4%
        45%
        100 bp
        1.4
        SRR15674236
        33.3%
        44%
        100 bp
        53.8
        SRR15674237
        0.0%
        0%
        0 bp
        0.0
        SRR15674238
        0.6%
        45%
        100 bp
        1.2
        SRR15674239
        12.9%
        45%
        100 bp
        40.0
        SRR15674240
        3.0%
        45%
        100 bp
        7.0
        SRR15674241
        0.0%
        0%
        0 bp
        0.0
        SRR15674242
        0.0%
        0%
        0 bp
        0.0
        SRR15674243
        0.0%
        0%
        0 bp
        0.0
        SRR15674244
        12.1%
        47%
        100 bp
        27.9
        SRR15674245
        22.5%
        47%
        100 bp
        14.6
        SRR15674246
        0.0%
        0%
        0 bp
        0.0
        SRR15674247
        27.6%
        44%
        100 bp
        64.7
        SRR15674248
        7.6%
        43%
        100 bp
        9.1
        SRR15674249
        10.1%
        44%
        100 bp
        26.7
        SRR15674250
        0.0%
        0%
        0 bp
        0.0
        SRR15674251
        11.8%
        46%
        100 bp
        45.7
        SRR15674252
        19.7%
        43%
        100 bp
        56.5
        SRR15674253
        15.7%
        45%
        100 bp
        36.6
        SRR15674254
        17.2%
        43%
        100 bp
        38.7

        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
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        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.

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        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.

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        Sequence Length Distribution

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

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        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.

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        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.

        223 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.

        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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