FastQCFastQC Report
Mon 5 Dec 2016
JM103_5_CAAAAG_L003_R1_001.fastq

Summary

[OK]Basic Statistics

MeasureValue
FilenameJM103_5_CAAAAG_L003_R1_001.fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences14729279
Sequences flagged as poor quality0
Sequence length50
%GC52

[OK]Per base sequence quality

Per base quality graph

[FAIL]Per tile sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[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

SequenceCountPercentagePossible Source
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC6942594.713462213595112RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA6856974.655333095394553RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA3820182.593596061287182RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA3467502.354154605938281RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGCTGGAATTCTCGGGTGCCAAGGAACTCC3206312.1768275283535603RNA PCR Primer, Index 1 (100% over 27bp)
CCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC2879751.9551194596829893RNA PCR Primer, Index 1 (100% over 33bp)
TCCTTCATTCCACCGGAGTCTGTGGAATTCTCGGGTGCCAAGGAACTCCA1992711.3528903892715998RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGCTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA1945581.3208928963868496RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA1916991.3014825776604544RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA1692591.1491329616337635RNA PCR Primer, Index 1 (100% over 28bp)
AACAGTAAGAGTTTATGTGCTGTGGAATTCTCGGGTGCCAAGGAACTCCA1423320.9663202116003099RNA PCR Primer, Index 1 (100% over 28bp)
TACCCTGTAGAACCGAATTTGCGTGGAATTCTCGGGTGCCAAGGAACTCC1284690.8722015517528048RNA PCR Primer, Index 1 (100% over 27bp)
ACAGTAGTCTGCACATTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG1186600.8056063029290165RNA PCR Primer, Index 1 (100% over 29bp)
TTTGGTCCCCTTCAACCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTCC1125020.7637984181031535RNA PCR Primer, Index 1 (100% over 27bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA1116160.7577831881655579No Hit
TTGGTCCCCTTCAACCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA1077950.7318416604098544RNA PCR Primer, Index 1 (100% over 28bp)
TAACGGAACCCATAATGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC1061960.7209857318881664RNA PCR Primer, Index 1 (100% over 27bp)
CTACGCCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCA1028270.6981129218884373RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG996840.6767744707666954RNA PCR Primer, Index 1 (100% over 29bp)
TACCCTGTAGAACCGAATTTGCTGGAATTCTCGGGTGCCAAGGAACTCCA976200.6627615649075559RNA PCR Primer, Index 1 (100% over 28bp)
CTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC812260.5514594434663095RNA PCR Primer, Index 2 (100% over 34bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC795890.5403455253987652No Hit
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGG728830.4948171597537123No Hit
TGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA723620.4912799872960516RNA PCR Primer, Index 7 (100% over 35bp)
TGAGGTAGTAGTTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA628510.4267079196476623RNA PCR Primer, Index 1 (100% over 28bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC599500.4070124545811102No Hit
ACCCTGTAGAACCGAATTTGCGTGGAATTCTCGGGTGCCAAGGAACTCCA598660.40644216190079635RNA PCR Primer, Index 1 (100% over 28bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTCTGGAATTCTCGGGTGC585650.3976094145545074No Hit
GCATCGATGGTTCAGTGGTAGAATGCTCGCCTTGGAATTCTCGGGTGCCA573650.38946237626431No Hit
TCCTTCATTCCACCGGAGTCTGTTGGAATTCTCGGGTGCCAAGGAACTCC554690.3765900557657982RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGTTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT543800.36919661851744406RNA PCR Primer, Index 1 (100% over 30bp)
TTCCCTTTGTCATCCTATGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA543470.3689725749644636RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT524230.3559101569058472RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG472550.3208235786693972RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTGGAATTCTCGGGTGCCAAGGAACTCC467090.3171166762473574RNA PCR Primer, Index 1 (100% over 27bp)
TACAGTAGTCTGCACATTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA464540.3153854306106904RNA PCR Primer, Index 1 (100% over 28bp)
TATGTGCCCTTGGACTACATCGTGGAATTCTCGGGTGCCAAGGAACTCCA455070.3089560595600097RNA PCR Primer, Index 1 (100% over 28bp)
ACAGTAGTCTGCACATTGGTTATGGAATTCTCGGGTGCCAAGGAACTCCA438700.2978421414924654RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCATTGCTGTCGGTGGGTGGAATTCTCGGGTGCCAAGGAACTCCA436830.2965725613589097RNA PCR Primer, Index 1 (100% over 28bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAA426800.28976299518801973RNA PCR Primer, Index 2 (97% over 36bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC426030.28924022689773204RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGCTGAAGAACTGCTGGAATTCTCGGGTGCCAAGGAACTCCA417280.28329967814446316RNA PCR Primer, Index 1 (100% over 28bp)
GCATCGATGGTTCAGTGGTAGAATGCTCTGGAATTCTCGGGTGCCAAGGA406450.27594697608756RNA PCR Primer, Index 1 (100% over 22bp)
TTCAAGTAATCCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA400510.2719141921339123RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC371910.2524970842089419No Hit
CCTGTCTGAGGGTCGCTTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA370290.25139723403976527RNA PCR Primer, Index 1 (100% over 32bp)
TTCACGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA366210.24862724102109818RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGCTGAAGAACTTGGAATTCTCGGGTGCCAAGGAACTCCAGT364690.24759528283767318RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTCTGCCTTGGAATTCTCGGGTGCC352820.23953650412895294No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA333410.2263586696945587No Hit
TACCCTGTAGATCCGGATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA316080.2145929885637987RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCAA312120.21190446592803353No Hit
TTCAGTCATTGTTTCTGGTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA304780.20692119417386282RNA PCR Primer, Index 1 (100% over 28bp)
CATTGCACTTGTCTCGGTCTGATGGAATTCTCGGGTGCCAAGGAACTCCA304640.2068261453938105RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGCTAAGTTCAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG299290.20319392415609752RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA297170.20175461405816264RNA PCR Primer, Index 1 (100% over 28bp)
GCATCGATGGTTCAGTGGTAGAATGCTGGAATTCTCGGGTGCCAAGGAAC293800.19946665413833223RNA PCR Primer, Index 1 (100% over 24bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG293710.19940555135115573RNA PCR Primer, Index 1 (100% over 29bp)
ACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA292620.1986655287064628RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCGTATGC264430.17952677792307417RNA PCR Primer, Index 28 (100% over 50bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC264150.17933668036296957RNA PCR Primer, Index 2 (100% over 34bp)
TTTGGTCCCCTTCAACCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCCA259790.17637658978419785RNA PCR Primer, Index 1 (100% over 28bp)
TGATGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA251500.1707483441653865RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC248260.16854864382703322No Hit
TTCACAGTGGTTAAGTTCTGCCTGGAATTCTCGGGTGCCAAGGAACTCCA247790.16822955149400048RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGTGGAATTCTCGGGTGCCAAGGAACTCCA247460.16800550794102007RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC244200.16579222920551645RNA PCR Primer, Index 1 (100% over 26bp)
TTTTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCT243880.16557497485111117RNA PCR Primer, Index 28 (100% over 43bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTTGGAATTCTCGGGTGCC238660.1620310131948753No Hit
TACCCTGTAGAACCGAATGTGTTGGAATTCTCGGGTGCCAAGGAACTCCA235790.16008251320380312RNA PCR Primer, Index 1 (100% over 28bp)
TTTGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGATCTCG231270.15701379544782879RNA PCR Primer, Index 28 (100% over 45bp)
AGCCTGTGATGATACAAGTTATCCCTGTCTGAACTCTGGTGTGGAATTCT230090.15621267001595937No Hit
TACCCTGTAGAACCGAATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC220050.14939631464649425RNA PCR Primer, Index 1 (100% over 27bp)
GCATCGATGGTTCAGTGGTAGAATGCTCGCCTGGAATTCTCGGGTGCCAA212990.1446031404524281No Hit
TGTAAACATCCCCGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC212590.14433157250942155RNA PCR Primer, Index 1 (100% over 26bp)
GTTTCCGTAGTGTAGTGGTTATCACGTCTGCCTGTGGAATTCTCGGGTGC211270.14343539829749982No Hit
TACCCTGTAGATCCGGATTTGTGTGGAATTCTCGGGTGCCAAGGAACTCC198550.13479953770989062RNA PCR Primer, Index 1 (100% over 27bp)
TACCATGTAGAACCGAATTTGTTGGAATTCTCGGGTGCCAAGGAACTCCA196180.13319049764757665RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGTTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG195830.13295287569744588RNA PCR Primer, Index 1 (100% over 29bp)
GAAGGATCATTATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAA193190.13116052727360247RNA PCR Primer, Index 28 (100% over 38bp)
TACGCCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAG192630.13078033215339324RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTTGGAATTCTCGGGTGCCAAGGAACTC190780.12952433041698783RNA PCR Primer, Index 1 (100% over 26bp)
TTCAAGTAATCCAGGATGGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA186310.1264895586538893RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG184410.12519961092460805RNA PCR Primer, Index 1 (100% over 29bp)
CTGGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA184280.1251113513431309RNA PCR Primer, Index 1 (100% over 32bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA183470.12456142625854259RNA PCR Primer, Index 7 (100% over 35bp)
TGAGGTAGTAGATTGAATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA181740.12338689490503914RNA PCR Primer, Index 1 (100% over 28bp)
TCCTTCATTCCACCGGAGTCTTGGAATTCTCGGGTGCCAAGGAACTCCAG180120.1222870447358625RNA PCR Primer, Index 1 (100% over 29bp)
TATTGCACTTGTCCCGGCCTGTTTGGAATTCTCGGGTGCCAAGGAACTCC180060.12224630954441151RNA PCR Primer, Index 1 (100% over 27bp)
AGCTACATCTGGCTACTGGGTCTCTGGAATTCTCGGGTGCCAAGGAACTC176830.12005339840463339RNA PCR Primer, Index 1 (100% over 26bp)
CCCAGTGTTCAGACTACCTGTTCTGGAATTCTCGGGTGCCAAGGAACTCC174230.11828820677509061RNA PCR Primer, Index 1 (100% over 27bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG172530.11713404301731266RNA PCR Primer, Index 1 (100% over 29bp)
TCCCTGAGACCCTTAACCTGTGATGGAATTCTCGGGTGCCAAGGAACTCC171250.11626502559969161RNA PCR Primer, Index 1 (100% over 27bp)
TCCAGCATCAGTGATTTTGTTGTGGAATTCTCGGGTGCCAAGGAACTCCA170660.11586446288375689RNA PCR Primer, Index 1 (100% over 28bp)
TGGACGGAGAACTGATAAGGGCTGGAATTCTCGGGTGCCAAGGAACTCCA169960.11538921898349538RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG165010.11202856568878897RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCATTGCTGTCGGTGGGTTTGGAATTCTCGGGTGCCAAGGAACTC164860.1119267277101615RNA PCR Primer, Index 1 (100% over 26bp)
AACCCGTAGATCCGAACTTGTGTGGAATTCTCGGGTGCCAAGGAACTCCA164510.11168910576003076RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTTGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA164020.11135643502984768RNA PCR Primer, Index 1 (100% over 28bp)
GCTTACGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGA161430.1095980325988801RNA PCR Primer, Index 28 (100% over 40bp)
AAGTTCTGTGATACACTCAGACTTGGAATTCTCGGGTGCCAAGGAACTCC160610.1090413183157166RNA PCR Primer, Index 1 (100% over 27bp)
CACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAA158580.10766311100495823RNA PCR Primer, Index 7 (97% over 37bp)
AGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAAAAGAT156260.10608801693552006RNA PCR Primer, Index 28 (100% over 41bp)
TTTTGTCCCCTTCAACCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTCC154800.10509679394354605RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA154760.10506963714924539RNA PCR Primer, Index 1 (100% over 28bp)
TTGTTCCCCTTCAACCAGCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA148860.10106400998989835RNA PCR Primer, Index 1 (100% over 28bp)

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
ACGTACC207.88635E-443.9695551
AACATTC1880650.043.9461751
ACGTTCG218650.043.89689324
AAACGCG207.971935E-443.8732833
CGTGTTA351.4808211E-743.8732832
AACAGTA159600.043.873131
TATAACG351.4809484E-743.87283720
GCATCGA180000.043.847421
TAGCTTA400850.043.8434071
GTTTCCG258800.043.825141
GTTCGCC218500.043.81884426
TCAACGC1802100.043.808626
TTCAACG1751400.043.801745
ACATTCA1899750.043.7982252
TCCTTCA306950.043.7976571
CAACGCT1803400.043.78927
CATTCAA1750700.043.785573
CGCTGTC1811550.043.779610
GCTTATC403500.043.7754253
GGTGAGT1628950.043.77467717