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        If you use plots from MultiQC in a publication or presentation, please cite:

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

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        About MultiQC

        This report was generated using MultiQC, version 1.0.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

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

         Loading report..

        Report generated on 2018-02-22, 14:02 based on data in: /mnt/gencore/sites/core-fastqc.bio.nyu.edu/html/HVHNVAFXX/merged


        General Statistics

        Showing 668 samples.

        loading..

        Run Statistics

        Run Statistics

        Showing 1/1 rows and 4/4 columns.
        Number of LanesTotal # of Single-End ReadsTotal # PF ReadsUndetermined % PhiX Aligned
        4.0
        187131897
        157319523
        5.5
        1.5

        Demultiplexing Report

        Demultiplexing Report
        Total Read Count: Total number of PF (Passing Filter) reads in this library.
        Portion: The proportion of reads that represent the individual library in the entire Library Pool.
        Perfect: The percentage of reads in this library which have a barcode perfectly matching the barcode specified in TuboWeb. The remainder of reads have mismatches upto the max number of mismatches specified in TuboWeb (Allowed barcode mismatch option in your Library Pool).

        Showing 334/334 rows and 3/3 columns.
        LibraryTotal Read CountPortion (%)Perfect (%)
        3031_d5_nw
        93713
        0.1
        94.8
        female_transmission_spleen_pcr2
        542484
        0.4
        95.9
        brain_ifn--_red_needle_e9_pcr2
        584722
        0.4
        94.7
        infko_m-black_spleen_pcr3
        294791
        0.2
        95.0
        liver_ifn--_red_needle_f11_pcr1
        1129683
        0.8
        96.7
        mosquito_18_pcr1
        828578
        0.6
        96.7
        spinal_cord_ifn--_red_needle_f6_pcr2
        398295
        0.3
        96.7
        infar_m-red_spinal_cord_pcr2
        954270
        0.6
        96.7
        2029_d3_nw
        239916
        0.2
        95.4
        infar_m-black_blood_pcr1
        561620
        0.4
        93.8
        infko_m-red_kidneys_pcr1
        417958
        0.3
        95.2
        infar_m-black_kidneys_pcr1
        543061
        0.4
        92.6
        male_transmission_liver_pcr1
        484833
        0.3
        95.3
        infko_m-black_bone_marrow_pcr1
        456585
        0.3
        93.8
        infko_m-red_kidneys_pcr3
        305256
        0.2
        94.3
        infar_m-black_reproductive_pcr3
        504873
        0.3
        94.2
        infko_m-black_bone_marrow_pcr3
        329532
        0.2
        95.9
        mosquito_19_f4_pcr2
        341187
        0.2
        95.4
        infar_m-black_brain_pcr2
        289813
        0.2
        95.3
        infar_m-black_brain_pcr1
        551059
        0.4
        94.3
        infko_m-red_spinal_cord_pcr2
        252946
        0.2
        96.5
        brain_ifn--_red_needle_f1_pcr2
        573046
        0.4
        96.5
        kidneys_fn--_red-b-red_transmission_pcr3
        533040
        0.4
        95.2
        3032_d5_nw
        353409
        0.2
        96.1
        male_transmission_brain_pcr1
        516867
        0.3
        95.5
        infar_m-black_bone_marrow_pcr2
        478949
        0.3
        95.7
        infar_f-red_blood_pcr1
        481694
        0.3
        94.3
        infar_m-red_reproductive_pcr1
        478340
        0.3
        95.4
        infko_m-black_kidneys_pcr2
        610169
        0.4
        95.7
        infko_m-black_spleen_pcr1
        412684
        0.3
        95.2
        spinal_cord_ifn--_red_needle_e10_pcr2
        630764
        0.4
        95.2
        spleen_ifn--_red_needle_pcr2
        505030
        0.3
        95.8
        infar_m-black_spinal_cord_pcr2
        533309
        0.4
        96.1
        spleen_ifn--_red_needle_pcr1
        610440
        0.4
        93.1
        2031_d1_nw
        220197
        0.1
        95.7
        female_transmission_spinal_cord_pcr2
        668105
        0.4
        95.8
        brain_ifn--_red_needle_f5_pcr2
        483287
        0.3
        96.1
        blood_meal_control_2_pcr2
        413120
        0.3
        95.7
        infar_m-red_kidneys_pcr1
        492861
        0.3
        94.3
        2031_d3_nw
        142400
        0.1
        95.0
        2033_d5_nw
        322898
        0.2
        96.5
        2038_d3_nw
        609378
        0.4
        95.7
        3034_d3_nw
        154834
        0.1
        93.4
        female_transmission_blood_pcr2
        357331
        0.2
        96.5
        infko_f-black_liver_pcr1
        878676
        0.6
        95.6
        3026_d5_nw
        177045
        0.1
        94.7
        spleen_fn--_red-b-red_transmission_g2_pcr1
        693143
        0.5
        94.6
        kidneys_ifn--_red_needle_pcr1
        442531
        0.3
        93.2
        infar_m-black_spleen_pcr3
        269813
        0.2
        95.1
        3022_d8_nw
        88450
        0.1
        92.9
        3034_d5_nw
        207517
        0.1
        93.8
        demux_negative_control_pcr1
        73.0
        0.0
        40.9
        mosquito_25_g3_pcr1
        854755
        0.6
        95.2
        3023_d8_nw
        237130
        0.2
        95.5
        mosquito_9_pcr2
        343284
        0.2
        95.1
        infko_m-black_kidneys_pcr3
        466584
        0.3
        94.0
        infar_m-red_bone_marrow_pcr1
        239573
        0.2
        91.1
        female_transmission_liver_pcr3
        404822
        0.3
        96.0
        spleen_fn--_red-b-red_transmission_g3_pcr2
        516120
        0.3
        95.5
        2032_d5_nw
        144507
        0.1
        94.8
        infar_m-red_spleen_pcr2
        596839
        0.4
        95.6
        spinal_cord_ifn--_red_needle_pcr1
        471405
        0.3
        93.2
        infar_m-black_blood_pcr2
        647842
        0.4
        95.5
        spinal_cord_fn--_red-b-red_transmission_pcr3
        452823
        0.3
        95.2
        cal-09_cb10-14_p2
        906686
        0.6
        95.6
        infar_m-red_kidneys_pcr2
        377146
        0.3
        96.5
        female_transmission_spleen_pcr1
        574274
        0.4
        94.8
        3032_d8_nw
        439046
        0.3
        94.2
        infko_f-black_spinal_cord_pcr2
        494214
        0.3
        96.0
        2043_d1_nw
        361015
        0.2
        94.8
        kidneys_fn--_red-b-red_transmission_pcr2
        625782
        0.4
        94.8
        3028_d8_nw
        145957
        0.1
        91.8
        infar_f-red_kidneys_pcr1
        560177
        0.4
        94.9
        2032_d-2_nw
        365711
        0.2
        92.7
        reproductive_ifn--_red_needle_pcr3
        331839
        0.2
        93.6
        infar_m-black_kidneys_pcr2
        433072
        0.3
        95.0
        2029_d1_nw
        264553
        0.2
        94.2
        3034_d1_nw
        363823
        0.2
        95.8
        female_transmission_spinal_cord_pcr1
        433779
        0.3
        94.7
        blood_meal_control_1_pcr1
        501013
        0.3
        95.9
        infar_m-black_liver_pcr1
        579783
        0.4
        94.6
        female_transmission_spleen_pcr3
        486363
        0.3
        95.8
        infar_m-red_blood_pcr1
        469018
        0.3
        94.6
        brain_ifn--_red-b-red_transmission_h1_pcr1
        568641
        0.4
        94.2
        infar_m-black_blood_pcr3
        586698
        0.4
        95.9
        3028_d5_nw
        282051
        0.2
        95.1
        infko_m-black_spinal_cord_pcr2
        275938
        0.2
        95.0
        infko_m-black_spinal_cord_pcr3
        363749
        0.2
        95.0
        negative_control_te_pcr2
        58.0
        0.0
        24.9
        liver_fn--_red-b-red_transmission_pcr2
        609144
        0.4
        95.6
        infar_m-black_spinal_cord_pcr1
        575003
        0.4
        95.3
        infar_f-red_spinal_cord_pcr2
        548779
        0.4
        95.6
        female_transmission_uterus_pcr2
        509701
        0.3
        96.3
        female_transmission_uterus_pcr3
        267503
        0.2
        95.8
        infko_f-black_bone_marrow_pcr1
        373940
        0.3
        95.1
        blood_ifn--_red_needle_f12_pcr1
        906739
        0.6
        96.3
        infko_m-black_reproductive_pcr1
        457455
        0.3
        95.1
        mosquito_19_e8_pcr2
        538952
        0.4
        93.7
        2039_d3_nw
        437495
        0.3
        94.3
        infko_m-red_reproductive_pcr1
        486752
        0.3
        94.4
        3027_d8_nw
        1203
        0.0
        96.5
        2041_d3_nw
        222832
        0.1
        93.5
        3026_d8_nw
        512453
        0.3
        94.1
        3031_d1_nw
        498736
        0.3
        95.6
        plasmid_control_pcr2
        582708
        0.4
        96.1
        infar_m-black_kidneys_pcr3
        477916
        0.3
        94.1
        male_transmission_brain_pcr3
        387987
        0.3
        95.9
        infar_f-red_reproductive_pcr1
        474731
        0.3
        95.0
        blood_ifn--_red_needle_g12_pcr1
        629640
        0.4
        93.1
        kidneys_fn--_red-b-red_transmission_pcr1
        450443
        0.3
        94.3
        liver_fn--_red-b-red_transmission_pcr1
        497929
        0.3
        93.5
        infko_m-red_liver_pcr1
        473301
        0.3
        95.0
        spleen_fn--_red-b-red_transmission_f3_pcr2
        354598
        0.2
        96.7
        mosquito_25_f9_pcr1
        436145
        0.3
        95.4
        2032_d1_nw
        384762
        0.3
        95.4
        female_transmission_overies_pcr3
        264165
        0.2
        95.5
        infko_m-red_bone_marrow_pcr2
        566078
        0.4
        94.6
        infko_f-black_reproductive_pcr3
        616188
        0.4
        95.6
        blood_meal_control_2_pcr3
        613443
        0.4
        95.8
        infar_m-black_spleen_pcr1
        488398
        0.3
        93.8
        3032_d-2_nw
        127118
        0.1
        96.2
        liver_ifn--_red_needle_pcr3
        569813
        0.4
        96.6
        viral_stock_control_pcr3
        531150
        0.4
        96.0
        spleen_fn--_red-b-red_transmission_h5_pcr1
        433099
        0.3
        92.2
        3033_d5_nw
        337972
        0.2
        95.7
        spinal_cord_ifn--_red_needle_f2_pcr2
        666755
        0.4
        96.4
        female_transmission_blood_pcr3
        254095
        0.2
        96.3
        infko_m-black_spinal_cord_pcr1
        476161
        0.3
        94.3
        reproductive_ifn--_red_needle_pcr2
        475537
        0.3
        96.1
        infko_m-red_bone_marrow_pcr3
        376142
        0.3
        94.2
        infko_m-black_blood_pcr2
        433014
        0.3
        95.1
        3030_d1_nw
        325223
        0.2
        94.9
        2040_d3_nw
        185012
        0.1
        95.5
        male_transmission_liver_pcr2
        559287
        0.4
        96.2
        infar_m-red_spinal_cord_pcr3
        694102
        0.5
        95.8
        infko_m-red_brain_pcr1
        417668
        0.3
        94.9
        kidneys_ifn--_red_needle_pcr2
        485482
        0.3
        95.3
        2030_d1_nw
        387495
        0.3
        95.4
        infar_f-red_liver_pcr1
        449368
        0.3
        94.4
        3030_d5_nw
        249079
        0.2
        96.1
        infko_m-red_bone_marrow_pcr1
        431921
        0.3
        94.8
        infar_f-red_bone_marrow_pcr3
        552526
        0.4
        95.6
        brain_ifn--_red-b-red_transmission_pcr2
        499774
        0.3
        96.3
        mosquito_1_pcr1
        478407
        0.3
        93.0
        infko_f-black_bone_marrow_pcr3
        382237
        0.3
        94.8
        female_transmission_brain_pcr2
        531255
        0.4
        94.9
        infko_f-black_brain_pcr1
        459875
        0.3
        95.2
        infko_m-red_spleen_pcr1
        457177
        0.3
        94.9
        infko_m-black_brain_pcr3
        948975
        0.6
        97.0
        mosquito_19_pcr3
        351210
        0.2
        95.6
        demux_negative_control_pcr2
        50.0
        0.0
        25.2
        infko_m-black_brain_pcr1
        403283
        0.3
        95.1
        mosquito_14_pcr1
        833986
        0.6
        96.5
        infko_f-black_brain_pcr2
        357323
        0.2
        95.3
        infar_f-red_reproductive_pcr3
        488727
        0.3
        95.8
        infko_m-black_spleen_pcr2
        762059
        0.5
        95.8
        male_transmission_kidney_pcr1
        583629
        0.4
        96.2
        pr8_cb10-14_p2
        231734
        0.2
        94.1
        plasmid_control_pcr1
        547354
        0.4
        95.1
        reproductive_ifn--_red_needle_g8_pcr1
        410608
        0.3
        93.5
        infar_m-red_bone_marrow_pcr2
        415510
        0.3
        96.1
        3033_d1_nw
        326212
        0.2
        96.7
        female_transmission_kidney_pcr1
        521000
        0.4
        95.7
        infko_f-black_bone_marrow_pcr2
        460261
        0.3
        93.7
        3024_d8_nw
        159241
        0.1
        93.0
        2036_d1_nw
        505783
        0.3
        96.6
        infar_m-black_reproductive_pcr2
        646702
        0.4
        95.9
        infko_m-black_brain_pcr2
        503140
        0.3
        95.3
        2037_d3_nw
        288345
        0.2
        95.8
        blood_meal_control_1_pcr2
        409288
        0.3
        95.5
        infar_f-red_blood_pcr2
        479035
        0.3
        96.0
        2029_d-2_nw
        479402
        0.3
        94.9
        infko_f-black_reproductive_pcr2
        548596
        0.4
        95.8
        infar_m-red_brain_pcr3
        372931
        0.3
        96.0
        infko_f-black_kidneys_pcr1
        490593
        0.3
        94.7
        3033_d8_nw
        464838
        0.3
        95.2
        liver_ifn--_red_needle_g10_pcr1
        577841
        0.4
        93.1
        3035_d5_nw
        199734
        0.1
        94.2
        infko_f-black_spinal_cord_pcr1
        589312
        0.4
        94.5
        infko_f-black_spleen_pcr1
        402992
        0.3
        95.5
        liver_fn--_red-b-red_transmission_pcr3
        533211
        0.4
        95.7
        brain_ifn--_red-b-red_transmission_g1_pcr1
        533449
        0.4
        92.3
        blood_meal_control_1_pcr3
        649065
        0.4
        96.3
        infko_f-black_blood_pcr2
        601675
        0.4
        95.3
        2039_d1_nw
        255615
        0.2
        95.3
        3031_d3_nw
        347742
        0.2
        95.3
        2030_d3_nw
        461266
        0.3
        95.3
        infar_f-red_kidneys_pcr2
        520553
        0.3
        95.8
        spinal_cord_fn--_red-b-red_transmission_pcr2
        614408
        0.4
        96.5
        negative_control_te_pcr1
        101.0
        0.0
        52.7
        2044_d1_nw
        530508
        0.4
        95.2
        infar_m-red_spleen_pcr1
        527549
        0.4
        94.2
        infar_m-red_reproductive_pcr3
        299077
        0.2
        95.7
        male_transmission_kidney_pcr3
        295094
        0.2
        95.6
        2034_d1_nw
        363545
        0.2
        95.7
        infko_f-black_reproductive_pcr1
        428956
        0.3
        94.2
        mosquito_4_pcr1
        886059
        0.6
        96.8
        liver_ifn--_red_needle_pcr2
        636406
        0.4
        96.6
        infko_m-red_spinal_cord_pcr3
        627812
        0.4
        95.8
        infar_m-black_reproductive_pcr1
        503833
        0.3
        95.0
        infar_m-red_blood_pcr2
        703967
        0.5
        96.3
        infar_m-black_bone_marrow_pcr3
        367070
        0.2
        96.1
        infar_m-red_liver_pcr1
        504639
        0.3
        97.7
        infko_f-black_brain_pcr3
        600058
        0.4
        95.4
        male_transmission_kidney_pcr2
        468657
        0.3
        96.5
        infar_f-red_spleen_pcr1
        557591
        0.4
        95.5
        3031_d8_nw
        80310
        0.1
        93.8
        mosquito_9_pcr3
        805554
        0.5
        96.3
        infko_m-black_bone_marrow_pcr2
        542492
        0.4
        95.8
        infko_m-red_blood_pcr2
        321367
        0.2
        96.2
        infar_m-black_bone_marrow_pcr1
        449779
        0.3
        92.3
        male_transmission_liver_pcr3
        704377
        0.5
        96.2
        infko_m-black_reproductive_pcr3
        297214
        0.2
        94.0
        infko_m-red_kidneys_pcr2
        545470
        0.4
        96.3
        infar_m-red_kidneys_pcr3
        384313
        0.3
        94.6
        2040_d1_nw
        306441
        0.2
        95.9
        2037_d1_nw
        508765
        0.3
        96.0
        2031_d-2_nw
        255149
        0.2
        95.7
        3035_d8_nw
        33235
        0.0
        93.6
        3032_d1_nw
        327443
        0.2
        94.5
        3031_d-2_nw
        256657
        0.2
        94.0
        2032_d3_nw
        175180
        0.1
        95.6
        3032_d3_nw
        206020
        0.1
        95.0
        2029_d5_nw
        315279
        0.2
        95.5
        infar_m-red_reproductive_pcr2
        616029
        0.4
        95.2
        mosquito_19_e12_pcr2
        491795
        0.3
        96.0
        infko_f-black_liver_pcr2
        665608
        0.4
        95.0
        3025_d8_nw
        1059270
        0.7
        94.9
        infko_m-red_brain_pcr2
        402756
        0.3
        96.2
        plasmid_control_pcr3
        546782
        0.4
        95.9
        2044_d3_nw
        341597
        0.2
        94.1
        ny238_plasmid_mix_cb10-14_p2
        613395
        0.4
        97.5
        brain_ifn--_red-b-red_transmission_pcr3
        584069
        0.4
        95.5
        infar_f-red_kidneys_pcr3
        369674
        0.2
        92.8
        negative_control_te_pcr3
        15.0
        0.0
        33.3
        2035_d1_nw
        837493
        0.6
        96.2
        male_transmission_testis_pcr1
        497392
        0.3
        93.6
        infar_f-red_bone_marrow_pcr2
        405191
        0.3
        95.4
        female_transmission_brain_pcr1
        439785
        0.3
        95.4
        female_transmission_bone_marrow_pcr3
        389600
        0.3
        95.0
        infko_m-red_reproductive_pcr2
        650707
        0.4
        96.0
        infko_m-black_blood_pcr3
        531353
        0.4
        96.1
        2038_d1_nw
        161490
        0.1
        95.8
        female_transmission_overies_pcr2
        655129
        0.4
        96.2
        2031_d5_nw
        222237
        0.1
        95.5
        2043_d3_nw
        344103
        0.2
        93.3
        2030_d5_nw
        112436
        0.1
        96.0
        spleen_ifn--_red_needle_pcr3
        854644
        0.6
        96.0
        infar_f-red_bone_marrow_pcr1
        490423
        0.3
        94.4
        infko_f-black_blood_pcr1
        539791
        0.4
        94.2
        infko_f-black_spinal_cord_pcr3
        556165
        0.4
        94.5
        3030_d8_nw
        234257
        0.2
        95.3
        2034_d3_nw
        236787
        0.2
        94.9
        2033_d1_nw
        216076
        0.1
        94.9
        infko_m-red_brain_pcr3
        533663
        0.4
        95.8
        female_transmission_uterus_pcr1
        521410
        0.4
        95.1
        mosquito_1_-_101817_pcr3
        720051
        0.5
        96.6
        infko_m-red_liver_pcr3
        390312
        0.3
        94.3
        female_transmission_brain_pcr3
        541051
        0.4
        96.0
        infko_m-black_blood_pcr1
        497224
        0.3
        95.7
        infko_m-black_liver_pcr1
        378590
        0.3
        95.1
        female_transmission_spinal_cord_pcr3
        493966
        0.3
        95.6
        mosquito_1_-_101817_pcr1
        451429
        0.3
        91.7
        mosquito_4_-_101817_pcr1
        682334
        0.5
        94.3
        3025_d5_nw
        359943
        0.2
        95.4
        2042_d1_nw
        257434
        0.2
        93.7
        infar_f-red_spinal_cord_pcr1
        497966
        0.3
        94.5
        infar_m-black_spinal_cord_pcr3
        342546
        0.2
        94.7
        3036_d3_nw
        372645
        0.3
        95.8
        infko_m-red_spleen_pcr3
        383139
        0.3
        93.0
        3035_d1_nw
        443360
        0.3
        95.4
        brain_ifn--_red_needle__pcr3
        536177
        0.4
        95.7
        brain_ifn--_red_needle__pcr1
        497296
        0.3
        93.7
        male_transmission_testis_pcr2
        490585
        0.3
        96.0
        3034_d8_nw
        330047
        0.2
        94.2
        2042_d3_nw
        301032
        0.2
        93.7
        3030_d-2_nw
        224606
        0.2
        95.7
        female_transmission_overies_pcr1
        537231
        0.4
        94.9
        infko_m-red_spinal_cord_pcr1
        572112
        0.4
        94.8
        male_transmission_spinal_cord_pcr2
        276300
        0.2
        95.2
        infko_f-black_kidneys_pcr2
        417583
        0.3
        95.8
        male_transmission_testis_pcr3
        283468
        0.2
        94.7
        3024_d5_nw
        435936
        0.3
        95.6
        3027_d5_nw
        193064
        0.1
        95.6
        male_transmission_spinal_cord_pcr1
        589177
        0.4
        93.6
        lp_negative_control_cb10-14_p2
        58.0
        0.0
        29.4
        spinal_cord_fn--_red-b-red_transmission_pcr1
        485757
        0.3
        94.4
        kidneys_ifn--_red_needle_pcr3
        432197
        0.3
        93.9
        3030_d3_nw
        298336
        0.2
        95.7
        3023_d5_nw
        272459
        0.2
        95.5
        infar_f-red_reproductive_pcr2
        423935
        0.3
        93.8
        infar_f-red_brain_pcr3
        451720
        0.3
        93.4
        infko_m-red_reproductive_pcr3
        297358
        0.2
        94.1
        spleen_fn--_red-b-red_transmission_pcr3
        473422
        0.3
        95.1
        infar_f-red_spleen_pcr3
        529155
        0.4
        95.0
        infar_m-black_brain_pcr3
        637268
        0.4
        95.9
        infar_m-red_bone_marrow_pcr3
        349314
        0.2
        96.3
        infar_m-red_brain_pcr1
        583503
        0.4
        94.8
        female_transmission_blood_pcr1
        525745
        0.4
        95.6
        3029_d8_nw
        145666
        0.1
        95.2
        blood_meal_control_2_pcr1
        476281
        0.3
        94.9
        female_transmission_kidney_pcr3
        520079
        0.3
        96.0
        viral_stock_control_pcr1
        480009
        0.3
        95.6
        3033_d3_nw
        183239
        0.1
        95.2
        2033_d3_nw
        215408
        0.1
        93.7
        demux_negative_control_pcr3
        11.0
        0.0
        18.8
        female_transmission_liver_pcr1
        579622
        0.4
        95.2
        spleen_fn--_red-b-red_transmission_pcr2
        485502
        0.3
        95.7
        female_transmission_liver_pcr2
        745044
        0.5
        96.7
        female_transmission_kidney_pcr2
        784185
        0.5
        96.6
        infar_m-red_spleen_pcr3
        440771
        0.3
        94.9
        infko_m-black_reproductive_pcr2
        492246
        0.3
        95.3
        2034_d5_nw
        483141
        0.3
        95.6
        2041_d1_nw
        306279
        0.2
        94.8
        infar_f-red_spinal_cord_pcr3
        555118
        0.4
        94.5
        infko_m-black_kidneys_pcr1
        395942
        0.3
        94.1
        infko_m-red_blood_pcr1
        479693
        0.3
        95.6
        male_transmission_spinal_cord_pcr3
        306270
        0.2
        94.1
        infko_f-black_liver_pcr3
        609427
        0.4
        95.2
        3021_d8_nw
        145144
        0.1
        95.0
        spinal_cord_ifn--_red_needle_pcr3
        467596
        0.3
        95.7
        3036_d1_nw
        252349
        0.2
        94.9
        3029_d3_nw
        350334
        0.2
        93.6
        infko_f-black_spleen_pcr3
        291263
        0.2
        93.5
        3036_d8_nw
        169163
        0.1
        95.0
        3035_d3_nw
        224575
        0.2
        96.3
        male_transmission_brain_pcr2
        492263
        0.3
        96.8
        infar_m-red_spinal_cord_pcr1
        562156
        0.4
        95.1
        reproductive_ifn--_red_needle_f10_pcr1
        887648
        0.6
        96.6
        3029_d1_nw
        412480
        0.3
        95.2
        3029_d-2_nw
        481467
        0.3
        95.2
        2030_d-2_nw
        148335
        0.1
        95.7
        3029_d5_nw
        749391
        0.5
        96.1
        viral_stock_control_pcr2
        473883
        0.3
        96.2

        FastQC

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

        Sequence Quality Histograms

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

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


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

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


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

        Click a heatmap row to see a line plot for that dataset.

        rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

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


        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.

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


        Sequence Length Distribution

        All samples have sequences of a single length (150bp).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.

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


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

        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. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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