HTSMultiQC-cleaning-report

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        Note that additional data was saved in HTSMultiQC-cleaning-report_multiqc_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 1.10.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        HTSMultiQC-cleaning-report

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-06-14, 10:13 based on data in: /share/workshop/mrnaseq_workshop/msettles/rnaseq_example/01-HTS_Preproc


        HTStream

        HTStream quality control and processing pipeline for High Throughput Sequencing data.

        Processing Overview

        General statistics from the HTStream pipeline.


        Preprocessing Statistics

        loading..

        Fragment Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

        loading..

        Basepair Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

        loading..

        hts_Stats

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 22/22 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        mouse_110_WT_C
        100.00%
        91.17%
        83.13%
        52.92%
        0.0010%
        initial stats
        mouse_110_WT_NC
        100.00%
        91.60%
        88.51%
        51.47%
        0.0012%
        initial stats
        mouse_148_WT_C
        100.00%
        93.02%
        87.44%
        51.34%
        0.0011%
        initial stats
        mouse_148_WT_NC
        100.00%
        90.50%
        86.38%
        52.19%
        0.0010%
        initial stats
        mouse_158_WT_C
        100.00%
        92.98%
        89.09%
        50.91%
        0.0008%
        initial stats
        mouse_158_WT_NC
        100.00%
        92.43%
        86.56%
        52.33%
        0.0009%
        initial stats
        mouse_183_KOMIR150_C
        100.00%
        93.14%
        87.45%
        51.91%
        0.0009%
        initial stats
        mouse_183_KOMIR150_NC
        100.00%
        91.48%
        82.11%
        54.19%
        0.0009%
        initial stats
        mouse_198_KOMIR150_C
        100.00%
        93.11%
        88.20%
        51.73%
        0.0011%
        initial stats
        mouse_198_KOMIR150_NC
        100.00%
        92.75%
        88.15%
        51.53%
        0.0009%
        initial stats
        mouse_206_KOMIR150_C
        100.00%
        90.60%
        72.35%
        56.37%
        0.0009%
        initial stats
        mouse_206_KOMIR150_NC
        100.00%
        86.34%
        77.66%
        56.02%
        0.0008%
        initial stats
        mouse_2670_KOTet3_C
        100.00%
        92.82%
        88.06%
        51.27%
        0.0007%
        initial stats
        mouse_2670_KOTet3_NC
        100.00%
        92.57%
        88.49%
        51.13%
        0.0009%
        initial stats
        mouse_7530_KOTet3_C
        100.00%
        92.75%
        86.49%
        51.62%
        0.0011%
        initial stats
        mouse_7530_KOTet3_NC
        100.00%
        92.06%
        86.86%
        51.13%
        0.0008%
        initial stats
        mouse_7531_KOTet3_C
        100.00%
        91.41%
        86.24%
        51.24%
        0.0007%
        initial stats
        mouse_7532_WT_NC
        100.00%
        93.26%
        87.83%
        51.32%
        0.0009%
        initial stats
        mouse_H510_WT_C
        100.00%
        92.09%
        85.76%
        52.19%
        0.0008%
        initial stats
        mouse_H510_WT_NC
        100.00%
        92.06%
        88.84%
        51.00%
        0.0010%
        initial stats
        mouse_H514_WT_C
        100.00%
        91.22%
        84.00%
        52.66%
        0.0009%
        initial stats
        mouse_H514_WT_NC
        100.00%
        92.70%
        86.45%
        51.26%
        0.0010%
        initial stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 22/22 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        mouse_110_WT_C
        101
        101
        mouse_110_WT_NC
        101
        101
        mouse_148_WT_C
        101
        101
        mouse_148_WT_NC
        101
        101
        mouse_158_WT_C
        101
        101
        mouse_158_WT_NC
        101
        101
        mouse_183_KOMIR150_C
        101
        101
        mouse_183_KOMIR150_NC
        101
        101
        mouse_198_KOMIR150_C
        101
        101
        mouse_198_KOMIR150_NC
        101
        101
        mouse_206_KOMIR150_C
        101
        101
        mouse_206_KOMIR150_NC
        101
        101
        mouse_2670_KOTet3_C
        101
        101
        mouse_2670_KOTet3_NC
        101
        101
        mouse_7530_KOTet3_C
        101
        101
        mouse_7530_KOTet3_NC
        101
        101
        mouse_7531_KOTet3_C
        101
        101
        mouse_7532_WT_NC
        101
        101
        mouse_H510_WT_C
        101
        101
        mouse_H510_WT_NC
        101
        101
        mouse_H514_WT_C
        101
        101
        mouse_H514_WT_NC
        101
        101

        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        loading..

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        loading..

        hts_SeqScreener

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 22/22 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        mouse_110_WT_C
        15
        0.0003%
        screen phix
        mouse_110_WT_NC
        14
        0.0003%
        screen phix
        mouse_148_WT_C
        11
        0.0002%
        screen phix
        mouse_148_WT_NC
        12
        0.0002%
        screen phix
        mouse_158_WT_C
        10
        0.0002%
        screen phix
        mouse_158_WT_NC
        8
        0.0002%
        screen phix
        mouse_183_KOMIR150_C
        13
        0.0003%
        screen phix
        mouse_183_KOMIR150_NC
        18
        0.0004%
        screen phix
        mouse_198_KOMIR150_C
        14
        0.0003%
        screen phix
        mouse_198_KOMIR150_NC
        16
        0.0003%
        screen phix
        mouse_206_KOMIR150_C
        32
        0.0006%
        screen phix
        mouse_206_KOMIR150_NC
        25
        0.0005%
        screen phix
        mouse_2670_KOTet3_C
        16
        0.0003%
        screen phix
        mouse_2670_KOTet3_NC
        14
        0.0003%
        screen phix
        mouse_7530_KOTet3_C
        19
        0.0004%
        screen phix
        mouse_7530_KOTet3_NC
        11
        0.0002%
        screen phix
        mouse_7531_KOTet3_C
        7
        0.0001%
        screen phix
        mouse_7532_WT_NC
        15
        0.0003%
        screen phix
        mouse_H510_WT_C
        11
        0.0002%
        screen phix
        mouse_H510_WT_NC
        17
        0.0003%
        screen phix
        mouse_H514_WT_C
        14
        0.0003%
        screen phix
        mouse_H514_WT_NC
        14
        0.0003%
        screen phix

        hts_SeqScreener 2

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 22/22 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        mouse_110_WT_C
        13283
        0.2657%
        count the number of rRNA reads
        mouse_110_WT_NC
        14314
        0.2863%
        count the number of rRNA reads
        mouse_148_WT_C
        19161
        0.3832%
        count the number of rRNA reads
        mouse_148_WT_NC
        25977
        0.5195%
        count the number of rRNA reads
        mouse_158_WT_C
        43066
        0.8613%
        count the number of rRNA reads
        mouse_158_WT_NC
        17941
        0.3588%
        count the number of rRNA reads
        mouse_183_KOMIR150_C
        19980
        0.3996%
        count the number of rRNA reads
        mouse_183_KOMIR150_NC
        22596
        0.4519%
        count the number of rRNA reads
        mouse_198_KOMIR150_C
        19178
        0.3836%
        count the number of rRNA reads
        mouse_198_KOMIR150_NC
        38401
        0.7680%
        count the number of rRNA reads
        mouse_206_KOMIR150_C
        14483
        0.2897%
        count the number of rRNA reads
        mouse_206_KOMIR150_NC
        16008
        0.3202%
        count the number of rRNA reads
        mouse_2670_KOTet3_C
        11012
        0.2202%
        count the number of rRNA reads
        mouse_2670_KOTet3_NC
        14161
        0.2832%
        count the number of rRNA reads
        mouse_7530_KOTet3_C
        25687
        0.5137%
        count the number of rRNA reads
        mouse_7530_KOTet3_NC
        6553
        0.1311%
        count the number of rRNA reads
        mouse_7531_KOTet3_C
        21880
        0.4376%
        count the number of rRNA reads
        mouse_7532_WT_NC
        17812
        0.3562%
        count the number of rRNA reads
        mouse_H510_WT_C
        13022
        0.2604%
        count the number of rRNA reads
        mouse_H510_WT_NC
        18736
        0.3747%
        count the number of rRNA reads
        mouse_H514_WT_C
        22774
        0.4555%
        count the number of rRNA reads
        mouse_H514_WT_NC
        19114
        0.3823%
        count the number of rRNA reads

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        Showing 22/22 rows and 3/3 columns.
        Sample Name% Duplicates% IgnoredNotes
        mouse_110_WT_C
        38.21%
        0.01%
        remove PCR duplicates
        mouse_110_WT_NC
        25.41%
        0.01%
        remove PCR duplicates
        mouse_148_WT_C
        26.60%
        0.01%
        remove PCR duplicates
        mouse_148_WT_NC
        30.69%
        0.01%
        remove PCR duplicates
        mouse_158_WT_C
        22.08%
        0.00%
        remove PCR duplicates
        mouse_158_WT_NC
        28.73%
        0.01%
        remove PCR duplicates
        mouse_183_KOMIR150_C
        32.76%
        0.00%
        remove PCR duplicates
        mouse_183_KOMIR150_NC
        49.15%
        0.01%
        remove PCR duplicates
        mouse_198_KOMIR150_C
        27.00%
        0.01%
        remove PCR duplicates
        mouse_198_KOMIR150_NC
        24.74%
        0.00%
        remove PCR duplicates
        mouse_206_KOMIR150_C
        61.04%
        0.00%
        remove PCR duplicates
        mouse_206_KOMIR150_NC
        71.84%
        0.00%
        remove PCR duplicates
        mouse_2670_KOTet3_C
        23.74%
        0.00%
        remove PCR duplicates
        mouse_2670_KOTet3_NC
        22.47%
        0.01%
        remove PCR duplicates
        mouse_7530_KOTet3_C
        29.47%
        0.01%
        remove PCR duplicates
        mouse_7530_KOTet3_NC
        21.02%
        0.00%
        remove PCR duplicates
        mouse_7531_KOTet3_C
        25.92%
        0.00%
        remove PCR duplicates
        mouse_7532_WT_NC
        24.49%
        0.00%
        remove PCR duplicates
        mouse_H510_WT_C
        29.44%
        0.00%
        remove PCR duplicates
        mouse_H510_WT_NC
        22.39%
        0.01%
        remove PCR duplicates
        mouse_H514_WT_C
        35.29%
        0.00%
        remove PCR duplicates
        mouse_H514_WT_NC
        24.99%
        0.01%
        remove PCR duplicates

        SuperDeduper: Duplicate Saturation

        Plots the number of duplicates against the number of unique reads per sample.

        loading..

        hts_AdapterTrimmer

        Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

        Showing 22/22 rows and 4/4 columns.
        Sample Name% Bp Lost% AdaptersAvg. Bps TrimmedNotes
        mouse_110_WT_C
        1.42%
        20.17%
        14.22
        trim adapters
        mouse_110_WT_NC
        1.35%
        20.19%
        13.55
        trim adapters
        mouse_148_WT_C
        1.19%
        17.82%
        13.50
        trim adapters
        mouse_148_WT_NC
        1.40%
        19.99%
        14.13
        trim adapters
        mouse_158_WT_C
        1.03%
        15.93%
        13.07
        trim adapters
        mouse_158_WT_NC
        1.14%
        16.49%
        13.99
        trim adapters
        mouse_183_KOMIR150_C
        1.17%
        17.44%
        13.54
        trim adapters
        mouse_183_KOMIR150_NC
        1.32%
        17.64%
        15.17
        trim adapters
        mouse_198_KOMIR150_C
        1.20%
        17.93%
        13.52
        trim adapters
        mouse_198_KOMIR150_NC
        1.13%
        17.11%
        13.36
        trim adapters
        mouse_206_KOMIR150_C
        1.55%
        19.10%
        16.44
        trim adapters
        mouse_206_KOMIR150_NC
        2.07%
        22.52%
        18.53
        trim adapters
        mouse_2670_KOTet3_C
        1.24%
        18.53%
        13.50
        trim adapters
        mouse_2670_KOTet3_NC
        1.13%
        16.88%
        13.54
        trim adapters
        mouse_7530_KOTet3_C
        1.32%
        19.67%
        13.54
        trim adapters
        mouse_7530_KOTet3_NC
        1.18%
        17.58%
        13.60
        trim adapters
        mouse_7531_KOTet3_C
        1.30%
        19.29%
        13.59
        trim adapters
        mouse_7532_WT_NC
        1.28%
        19.12%
        13.50
        trim adapters
        mouse_H510_WT_C
        1.30%
        18.91%
        13.87
        trim adapters
        mouse_H510_WT_NC
        1.09%
        16.11%
        13.69
        trim adapters
        mouse_H514_WT_C
        1.71%
        22.55%
        15.35
        trim adapters
        mouse_H514_WT_NC
        1.16%
        17.55%
        13.35
        trim adapters

        AdapterTrimmer: Trimmed Basepairs Composition

        Composition of basepairs trimmed from the ends of paired end and single end reads.

        loading..

        hts_PolyATTrim

        Attempts to trim poly-A and poly-T sequences from the end of reads.

        Showing 22/22 rows and 4/4 columns.
        Sample NameTotal Bp Lost% R1 of Bp Lost% R2 of Bp LostNotes
        mouse_110_WT_C
        60982
        0.00%
        100.00%
        remove polyA
        mouse_110_WT_NC
        69529
        0.00%
        100.00%
        remove polyA
        mouse_148_WT_C
        71536
        0.00%
        100.00%
        remove polyA
        mouse_148_WT_NC
        64607
        0.00%
        100.00%
        remove polyA
        mouse_158_WT_C
        70958
        0.00%
        100.00%
        remove polyA
        mouse_158_WT_NC
        64439
        0.00%
        100.00%
        remove polyA
        mouse_183_KOMIR150_C
        59702
        0.00%
        100.00%
        remove polyA
        mouse_183_KOMIR150_NC
        47637
        0.00%
        100.00%
        remove polyA
        mouse_198_KOMIR150_C
        66362
        0.00%
        100.00%
        remove polyA
        mouse_198_KOMIR150_NC
        67756
        0.00%
        100.00%
        remove polyA
        mouse_206_KOMIR150_C
        40112
        0.00%
        100.00%
        remove polyA
        mouse_206_KOMIR150_NC
        31238
        0.00%
        100.00%
        remove polyA
        mouse_2670_KOTet3_C
        67383
        0.00%
        100.00%
        remove polyA
        mouse_2670_KOTet3_NC
        72127
        0.00%
        100.00%
        remove polyA
        mouse_7530_KOTet3_C
        67055
        0.00%
        100.00%
        remove polyA
        mouse_7530_KOTet3_NC
        73894
        0.00%
        100.00%
        remove polyA
        mouse_7531_KOTet3_C
        74263
        0.00%
        100.00%
        remove polyA
        mouse_7532_WT_NC
        73285
        0.00%
        100.00%
        remove polyA
        mouse_H510_WT_C
        66063
        0.00%
        100.00%
        remove polyA
        mouse_H510_WT_NC
        70893
        0.00%
        100.00%
        remove polyA
        mouse_H514_WT_C
        62232
        0.00%
        100.00%
        remove polyA
        mouse_H514_WT_NC
        76557
        0.00%
        100.00%
        remove polyA

        hts_NTrimmer

        Trims reads to the longest subsequence that contains no N's.

        Showing 22/22 rows and 5/5 columns.
        Sample NameTotal Bp Lost% R1 of Bp Lost% R2 of Bp Lost% DiscardedNotes
        mouse_110_WT_C
        6913
        34.31%
        65.69%
        0.00%
        remove any remaining N characters
        mouse_110_WT_NC
        9431
        35.87%
        64.13%
        0.00%
        remove any remaining N characters
        mouse_148_WT_C
        8573
        35.25%
        64.75%
        0.00%
        remove any remaining N characters
        mouse_148_WT_NC
        8211
        32.42%
        67.58%
        0.00%
        remove any remaining N characters
        mouse_158_WT_C
        11233
        37.51%
        62.49%
        0.00%
        remove any remaining N characters
        mouse_158_WT_NC
        8895
        32.76%
        67.24%
        0.00%
        remove any remaining N characters
        mouse_183_KOMIR150_C
        7888
        31.54%
        68.46%
        0.00%
        remove any remaining N characters
        mouse_183_KOMIR150_NC
        6254
        28.21%
        71.79%
        0.00%
        remove any remaining N characters
        mouse_198_KOMIR150_C
        8778
        34.20%
        65.80%
        0.00%
        remove any remaining N characters
        mouse_198_KOMIR150_NC
        8884
        31.92%
        68.08%
        0.00%
        remove any remaining N characters
        mouse_206_KOMIR150_C
        5216
        31.84%
        68.16%
        0.00%
        remove any remaining N characters
        mouse_206_KOMIR150_NC
        3456
        32.03%
        67.97%
        0.00%
        remove any remaining N characters
        mouse_2670_KOTet3_C
        8668
        37.32%
        62.68%
        0.00%
        remove any remaining N characters
        mouse_2670_KOTet3_NC
        8421
        34.22%
        65.78%
        0.00%
        remove any remaining N characters
        mouse_7530_KOTet3_C
        8260
        36.53%
        63.47%
        0.00%
        remove any remaining N characters
        mouse_7530_KOTet3_NC
        11298
        35.37%
        64.63%
        0.00%
        remove any remaining N characters
        mouse_7531_KOTet3_C
        9762
        41.46%
        58.54%
        0.00%
        remove any remaining N characters
        mouse_7532_WT_NC
        8688
        33.17%
        66.83%
        0.00%
        remove any remaining N characters
        mouse_H510_WT_C
        7780
        32.75%
        67.25%
        0.00%
        remove any remaining N characters
        mouse_H510_WT_NC
        9069
        33.64%
        66.36%
        0.00%
        remove any remaining N characters
        mouse_H514_WT_C
        7332
        35.73%
        64.27%
        0.00%
        remove any remaining N characters
        mouse_H514_WT_NC
        9950
        27.15%
        72.85%
        0.00%
        remove any remaining N characters

        NTrimmer: Trimmed Basepairs Composition

        Plots the number of N bases trimmed from ends of paired end and single end reads.

           
        loading..

        hts_QWindowTrim

        Uses a sliding window approach to remove the low quality ends of reads.

        Showing 22/22 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        mouse_110_WT_C
        0.65%
        6.22%
        93.78%
        1.30
        quality trim the ends of reads
        mouse_110_WT_NC
        0.52%
        7.02%
        92.98%
        1.03
        quality trim the ends of reads
        mouse_148_WT_C
        0.58%
        6.11%
        93.89%
        1.15
        quality trim the ends of reads
        mouse_148_WT_NC
        0.59%
        6.29%
        93.71%
        1.17
        quality trim the ends of reads
        mouse_158_WT_C
        0.48%
        7.59%
        92.41%
        0.97
        quality trim the ends of reads
        mouse_158_WT_NC
        0.56%
        6.92%
        93.08%
        1.12
        quality trim the ends of reads
        mouse_183_KOMIR150_C
        0.59%
        5.91%
        94.09%
        1.18
        quality trim the ends of reads
        mouse_183_KOMIR150_NC
        0.67%
        5.78%
        94.22%
        1.34
        quality trim the ends of reads
        mouse_198_KOMIR150_C
        0.51%
        6.86%
        93.14%
        1.02
        quality trim the ends of reads
        mouse_198_KOMIR150_NC
        0.52%
        6.92%
        93.08%
        1.04
        quality trim the ends of reads
        mouse_206_KOMIR150_C
        0.86%
        6.15%
        93.85%
        1.70
        quality trim the ends of reads
        mouse_206_KOMIR150_NC
        1.00%
        5.48%
        94.52%
        1.98
        quality trim the ends of reads
        mouse_2670_KOTet3_C
        0.53%
        7.07%
        92.93%
        1.05
        quality trim the ends of reads
        mouse_2670_KOTet3_NC
        0.49%
        7.79%
        92.21%
        0.97
        quality trim the ends of reads
        mouse_7530_KOTet3_C
        0.59%
        6.28%
        93.72%
        1.17
        quality trim the ends of reads
        mouse_7530_KOTet3_NC
        0.50%
        8.04%
        91.96%
        1.00
        quality trim the ends of reads
        mouse_7531_KOTet3_C
        0.58%
        6.48%
        93.52%
        1.16
        quality trim the ends of reads
        mouse_7532_WT_NC
        0.52%
        7.03%
        92.97%
        1.04
        quality trim the ends of reads
        mouse_H510_WT_C
        0.57%
        6.75%
        93.25%
        1.14
        quality trim the ends of reads
        mouse_H510_WT_NC
        0.46%
        7.92%
        92.08%
        0.91
        quality trim the ends of reads
        mouse_H514_WT_C
        0.61%
        6.10%
        93.90%
        1.21
        quality trim the ends of reads
        mouse_H514_WT_NC
        0.58%
        6.44%
        93.56%
        1.16
        quality trim the ends of reads

        QWindowTrim: Trimmed Basepairs Composition

        Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

           
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        hts_LengthFilter

        Discards reads below a minimum length threshold.

        Showing 22/22 rows and 2/2 columns.
        Sample Name% PE LostNotes
        mouse_110_WT_C
        1.27%
        remove reads < 50bp
        mouse_110_WT_NC
        0.97%
        remove reads < 50bp
        mouse_148_WT_C
        1.06%
        remove reads < 50bp
        mouse_148_WT_NC
        1.15%
        remove reads < 50bp
        mouse_158_WT_C
        0.85%
        remove reads < 50bp
        mouse_158_WT_NC
        1.06%
        remove reads < 50bp
        mouse_183_KOMIR150_C
        1.10%
        remove reads < 50bp
        mouse_183_KOMIR150_NC
        1.39%
        remove reads < 50bp
        mouse_198_KOMIR150_C
        0.95%
        remove reads < 50bp
        mouse_198_KOMIR150_NC
        0.95%
        remove reads < 50bp
        mouse_206_KOMIR150_C
        1.69%
        remove reads < 50bp
        mouse_206_KOMIR150_NC
        2.34%
        remove reads < 50bp
        mouse_2670_KOTet3_C
        0.96%
        remove reads < 50bp
        mouse_2670_KOTet3_NC
        0.88%
        remove reads < 50bp
        mouse_7530_KOTet3_C
        1.09%
        remove reads < 50bp
        mouse_7530_KOTet3_NC
        0.92%
        remove reads < 50bp
        mouse_7531_KOTet3_C
        1.08%
        remove reads < 50bp
        mouse_7532_WT_NC
        0.96%
        remove reads < 50bp
        mouse_H510_WT_C
        1.07%
        remove reads < 50bp
        mouse_H510_WT_NC
        0.85%
        remove reads < 50bp
        mouse_H514_WT_C
        1.32%
        remove reads < 50bp
        mouse_H514_WT_NC
        1.07%
        remove reads < 50bp

        hts_Stats 2

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 22/22 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        mouse_110_WT_C
        100.00%
        95.91%
        93.29%
        50.20%
        0.0000%
        final stats
        mouse_110_WT_NC
        100.00%
        96.15%
        94.53%
        50.24%
        0.0000%
        final stats
        mouse_148_WT_C
        100.00%
        96.11%
        94.12%
        49.91%
        0.0000%
        final stats
        mouse_148_WT_NC
        100.00%
        96.10%
        94.15%
        50.16%
        0.0000%
        final stats
        mouse_158_WT_C
        100.00%
        95.80%
        94.15%
        49.99%
        0.0000%
        final stats
        mouse_158_WT_NC
        100.00%
        95.91%
        93.77%
        50.20%
        0.0000%
        final stats
        mouse_183_KOMIR150_C
        100.00%
        96.32%
        94.41%
        50.18%
        0.0000%
        final stats
        mouse_183_KOMIR150_NC
        100.00%
        96.03%
        93.43%
        50.39%
        0.0000%
        final stats
        mouse_198_KOMIR150_C
        100.00%
        96.25%
        94.62%
        50.23%
        0.0000%
        final stats
        mouse_198_KOMIR150_NC
        100.00%
        95.97%
        93.96%
        50.34%
        0.0000%
        final stats
        mouse_206_KOMIR150_C
        100.00%
        95.23%
        92.27%
        50.00%
        0.0000%
        final stats
        mouse_206_KOMIR150_NC
        100.00%
        95.13%
        91.85%
        50.21%
        0.0000%
        final stats
        mouse_2670_KOTet3_C
        100.00%
        95.95%
        94.13%
        50.03%
        0.0000%
        final stats
        mouse_2670_KOTet3_NC
        100.00%
        95.85%
        94.15%
        50.00%
        0.0000%
        final stats
        mouse_7530_KOTet3_C
        100.00%
        96.13%
        94.16%
        49.86%
        0.0000%
        final stats
        mouse_7530_KOTet3_NC
        100.00%
        95.44%
        93.08%
        49.83%
        0.0000%
        final stats
        mouse_7531_KOTet3_C
        100.00%
        95.86%
        93.26%
        49.73%
        0.0000%
        final stats
        mouse_7532_WT_NC
        100.00%
        96.26%
        94.62%
        49.83%
        0.0000%
        final stats
        mouse_H510_WT_C
        100.00%
        96.05%
        94.07%
        49.84%
        0.0000%
        final stats
        mouse_H510_WT_NC
        100.00%
        96.10%
        94.80%
        49.76%
        0.0000%
        final stats
        mouse_H514_WT_C
        100.00%
        96.18%
        94.27%
        49.82%
        0.0000%
        final stats
        mouse_H514_WT_NC
        100.00%
        96.06%
        93.63%
        49.73%
        0.0000%
        final stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

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        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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