FastQCFastQC Report
Fri 30 Sep 2016
D1_S2_L001_R1_001.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename D1_S2_L001_R1_001.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 50338844
Filtered Sequences 0
Sequence length 100
%GC 44

[FAIL] Per base sequence quality

Per base quality graph

[OK] Per sequence quality scores

Per Sequence quality graph

[FAIL] Per base sequence content

Per base sequence content

[FAIL] Per base GC content

Per base GC content graph

[WARN] Per sequence GC content

Per sequence GC content graph

[OK] Per base N content

N content graph

[OK] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[FAIL] Overrepresented sequences

Sequence Count Percentage Possible Source
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 25788115 51.22905682935428 TruSeq Adapter, Index 1 (97% over 35bp)
GAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCCGT 1060390 2.106504471973969 TruSeq Adapter, Index 1 (96% over 30bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATATCGTAT 906763 1.8013186794674902 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAACTCGTAT 522755 1.0384723971809922 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAGCTCGTAT 488006 0.9694422064996169 TruSeq Adapter, Index 1 (97% over 35bp)
NATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 476574 0.946732110097721 TruSeq Adapter, Index 6 (97% over 34bp)
CGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCC 430528 0.8552600055734296 TruSeq Adapter, Index 1 (96% over 32bp)
GATCGGAAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 347258 0.6898410301198017 TruSeq Adapter, Index 6 (96% over 30bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGACCTCGTAT 316818 0.6293708294135638 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAACGATCTCGTATG 254725 0.5060207580452185 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACATCTCGTATG 252017 0.5006412145658331 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 200169 0.3976432196178363 TruSeq Adapter, Index 1 (96% over 31bp)
GAATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 198436 0.3942005501755265 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAGATCTCGTATG 190246 0.37793080826409126 TruSeq Adapter, Index 1 (97% over 35bp)
ATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 181114 0.3597897480522199 TruSeq Adapter, Index 1 (97% over 34bp)
GATCGGAAGGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 161073 0.3199775505373147 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
GATCGGAAGAAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 133161 0.26452931656515594 TruSeq Adapter, Index 6 (96% over 26bp)
GATCGGAAGAGCACACGTCTGAACTCAGTCACGTGAAACGATCTCGTATG 121322 0.24101069941137304 Illumina Multiplexing PCR Primer 2.01 (96% over 26bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAAATCGTAT 109299 0.21712655936238823 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGTACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 101485 0.2016037555411483 TruSeq Adapter, Index 6 (97% over 34bp)
TGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCC 99347 0.1973565384218994 TruSeq Adapter, Index 6 (96% over 31bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAATGATCTCGTAT 99210 0.19708438278797186 TruSeq Adapter, Index 1 (97% over 35bp)
GGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATGCCG 98735 0.19614077748785808 TruSeq Adapter, Index 1 (96% over 31bp)
GATCGGAAGACACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 96411 0.19152406439845937 TruSeq Adapter, Index 1 (95% over 24bp)
GATCGGAAGAGCACAACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 94032 0.18679809174799486 TruSeq Adapter, Index 1 (95% over 21bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCATGTGAAACGATCTCGTAT 93909 0.18655374763870222 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCATCACGTGAAACGATCTCGTATG 93328 0.18539956936635255 Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
GATCGGAAGAGCACACGTCTGAAACTCCAGTCACGTGAAACGATCTCGTA 91078 0.1809298600500242 Illumina Multiplexing PCR Primer 2.01 (95% over 23bp)
GATCGGAAGAGCACATGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 89602 0.17799773073851277 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCAACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 86949 0.17272744682019317 TruSeq Adapter, Index 1 (95% over 23bp)
GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 85089 0.16903248711869504 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 83828 0.16652746336407726 TruSeq Adapter, Index 1 (96% over 25bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGC 81943 0.16278284022573106 TruSeq Adapter, Index 6 (100% over 50bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGAGATCGTAT 79203 0.15733972754718006 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATTCGTATG 74061 0.1471249518562643 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 72969 0.14495565293473964 TruSeq Adapter, Index 1 (96% over 26bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAACGATCTCGTA 72909 0.1448364606863042 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCATACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 71390 0.1418189102634141 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGACACGATCTCGTAT 70474 0.13999924193729996 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 69403 0.13787166030272766 No Hit
GATCGGAAGAGCACACGTCTGAACTCTAGTCACGTGAAACGATCTCGTAT 67450 0.13399195261615462 TruSeq Adapter, Index 6 (97% over 34bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTA 66888 0.1328755185558095 TruSeq Adapter, Index 1 (97% over 35bp)
GATTGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 66529 0.1321623516026709 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCAGGTCACGTGAAACGATCTCGTA 62889 0.12493135519758858 Illumina Multiplexing PCR Primer 2.01 (96% over 29bp)
GATCGGAAGAGCACACGTCTGAACTTCAGTCACGTGAAACGATCTCGTAT 62657 0.12447047850363827 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTTACGTGAAACGATCTCGTAT 61888 0.12294283118619093 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTTTGAACTCCAGTCACGTGAAACGATCTCGTAT 60060 0.11931144068385838 TruSeq Adapter, Index 6 (97% over 34bp)
GATGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 59702 0.11860026026819369 TruSeq Adapter, Index 6 (96% over 31bp)
GATCGGAAGAGCACACGTCTGAACTCCAAGTCACGTGAAACGATCTCGTA 59412 0.1180241644007558 Illumina Multiplexing PCR Primer 2.01 (96% over 28bp)
GATCGGAAGAGCACACGTCTGAACTCCCAGTCACGTGAAACGATCTCGTA 58691 0.11659187088205682 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
GATCGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 57671 0.11456560265865462 TruSeq Adapter, Index 1 (96% over 30bp)
GATCGGAAGAGCACACGTCTGAATTCCAGTCACGTGAAACGATCTCGTAT 56339 0.11191953474338824 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGACATCGTAT 56196 0.11163545988461714 TruSeq Adapter, Index 1 (97% over 35bp)
GATCGGAAGAGCACACGTCTGGAACTCCAGTCACGTGAAACGATCTCGTA 54023 0.1073187139537809 Illumina Multiplexing PCR Primer 2.01 (95% over 23bp)
AATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTAT 53029 0.10534409570470073 TruSeq Adapter, Index 6 (97% over 34bp)
GATCGGAAGAGCACACGTCTGAATCCAGTCACGTGAAACGATCTCGTATG 52079 0.10345688510447319 Illumina Multiplexing PCR Primer 2.01 (95% over 23bp)
GACGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAACGATCTCGTATG 52036 0.10337146399309449 TruSeq Adapter, Index 1 (96% over 32bp)
GATCGGAAGAGCACACGTCTAACTCCAGTCACGTGAAACGATCTCGTATG 51601 0.10250732019193767 Illumina Multiplexing PCR Primer 2.01 (95% over 22bp)

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
CGTCT 94413945 39.38585 313.13025 15-19
CACGT 103086735 25.887896 185.08495 10-14
GTCTG 52729670 23.080917 332.23853 15-19
GTCTT 43197530 19.994804 323.32944 50-54
TTCTG 42930465 19.871185 333.77368 55-59
TGCTT 42248075 19.55533 299.16483 60-64
TCTTC 43576785 19.222927 290.97144 55-59
CTTCT 43108510 19.016357 311.32925 55-59
GCTTG 42404290 18.561274 306.7476 60-64
TCTGC 42910600 17.900646 308.18738 55-59
CTGCT 42704345 17.814604 289.52597 55-59
CTCGT 42063915 17.547441 283.27972 40-44
TGCCG 43482110 17.153572 262.02838 50-54
GCCGT 43058875 16.986605 281.47266 50-54
TCTCG 40251315 16.791294 286.36868 40-44
CCGTC 43579295 16.38439 274.9961 50-54
AAAAA 359704155 15.444249 114.79079 70-74
TCTGA 53122730 14.802272 215.62428 15-19
ACGTG 52053070 13.716209 194.20839 30-34
TCCAG 53384580 13.406323 180.10509 25-29
TCACG 53261910 13.375518 177.47623 30-34
CAGTC 53151010 13.347669 189.2473 25-29
GTCAC 53014330 13.313345 180.69344 25-29
ACGTC 52863985 13.275589 183.62025 15-19
CCAGT 52821005 13.264794 186.75143 25-29
CGTGA 50194605 13.226496 196.66646 30-34
GTATG 44600455 13.040107 217.47984 45-49
ACTCC 53106300 12.710015 184.02768 20-24
CTCCA 53030215 12.691805 173.50912 20-24
CGTAT 44245040 12.328566 201.92163 45-49
TATGC 44125090 12.295142 210.74028 45-49
TCGTA 43740025 12.187846 186.34772 45-49
TCGGA 43976155 11.587907 968.6298 3
ATCGG 43703730 11.516122 975.8164 2
GATCG 42990605 11.328211 974.44464 1
GATCT 39654560 11.04946 182.42572 40-44
ATGCC 43912140 11.027536 177.08957 45-49
CTTGA 39451070 10.992761 181.81976 60-64
ATCTC 40420330 10.73381 179.41898 40-44
CGATC 39244495 9.855364 154.17796 40-44
TGAAA 86497705 9.691392 76.52083 35-39
CTGAA 55592950 9.325185 123.24582 15-19
TGAAC 54733600 9.181038 121.72103 20-24
GAACT 54641090 9.165518 126.254395 20-24
AGTCA 53587505 8.9887905 128.64749 25-29
GTGAA 50154985 8.827663 123.52516 30-34
AACTC 54975695 8.788497 121.96843 20-24
GGAAG 49197350 8.188665 603.3299 5
ACACG 52729135 7.9713945 116.35267 10-14
GAGCA 49967600 7.9262185 558.1371 9
AGAGC 49675235 7.879841 559.88385 8
CACAC 54380100 7.834834 108.849785 10-14
GCACA 50634495 7.6547346 113.344215 10-14
AGCAC 50395240 7.618565 110.946625 10-14
CGGAA 46015455 7.2993 582.26385 4
TTGAA 37317320 6.9454803 115.6342 60-64
ACGAT 40681665 6.8239594 108.35181 35-39
AAGAG 54635780 5.7889333 377.31168 7
GAAGA 52623825 5.575756 381.1318 6
GAAAC 47982315 4.845166 71.32645 35-39
AAACG 47194585 4.765623 71.91554 35-39
AACGA 45202630 4.564479 73.59383 35-39
TTTTT 6644220 3.6084146 9.074558 90-94
GAAAA 48753255 3.2883267 38.837685 65-69
CTTGG 4339270 1.8993924 28.157537 60-64
AAAAG 23037060 1.5538119 10.101463 75-79
AAAGA 19173050 1.2931907 7.573276 75-79
AAAAC 20014735 1.286552 7.736506 70-74
TTGGA 4336830 1.2679853 17.60775 60-64
TGGAA 6530815 1.1494737 8.224928 60-64
AAACA 15430665 0.99188685 6.066849 75-79
AAAAT 13854815 0.9881714 5.531049 75-79
TTGAT 2747530 0.84946305 11.533235 60-64
GGGGG 1943845 0.7984232 5.134747 95-96
TGATC 2783675 0.7756513 8.981977 60-64
GGAAA 7268200 0.77010196 7.0514235 5
GAAAG 6836760 0.72438884 6.438768 6
GCTCG 1576955 0.62210435 5.992041 40-44
ATCGT 2208535 0.61539257 8.645606 40-44
TATCG 1730695 0.48224583 6.3771696 40-44
GGAGC 1737305 0.43291602 5.461956 9
TCGGG 739885 0.30626827 12.546404 3
CGGGA 1184770 0.29523078 7.408174 4
AATCG 1495450 0.2508474 5.017333 2
Produced by FastQC (version 0.10.1)