FastQCFastQC Report
Mon 5 Dec 2016
JM61_3_CCGTCC_L004_R1_001.fastq

Summary

[OK]Basic Statistics

MeasureValue
FilenameJM61_3_CCGTCC_L004_R1_001.fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences17100867
Sequences flagged as poor quality0
Sequence length50
%GC53

[OK]Per base sequence quality

Per base quality graph

[OK]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

[FAIL]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
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTATGC445098226.027814847048397RNA PCR Primer, Index 16 (100% over 50bp)
ATGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG5147353.0099935868748644RNA PCR Primer, Index 1 (100% over 29bp)
ATGACCTATGAATTGACAGCCATGGAATTCTCGGGTGCCAAGGAACTCCA5041792.948265722433839RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGCTGGAATTCTCGGGTGCCAAGGAACTCC4689632.7423346430330113RNA PCR Primer, Index 1 (100% over 27bp)
TAACGGAACCCATAATGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC3270521.9124878288334737RNA PCR Primer, Index 1 (100% over 27bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA2759381.613590702740393RNA PCR Primer, Index 1 (100% over 28bp)
TGAGAACTGAATTCCATAGATGGTGGAATTCTCGGGTGCCAAGGAACTCC1840101.076027314872398RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA1719191.0053232973509472RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCA1224230.7158876798468756RNA PCR Primer, Index 1 (100% over 28bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCATCTCGTAT1138800.6659311484031775RNA PCR Primer, Index 16 (100% over 48bp)
TAGCTTATCAGACTGGTGTTGGTGGAATTCTCGGGTGCCAAGGAACTCCA1081600.6324825519080407RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGG1077630.6301610321862628No Hit
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA1013120.5924377986215552RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA986000.5765789535700149RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC979960.5730469689051438RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA881880.5156931516980982RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGCTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA870510.5090443659961802RNA PCR Primer, Index 1 (100% over 28bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTTGGAATTCT749730.43841636801221834No Hit
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG739960.43270320738708745RNA PCR Primer, Index 1 (100% over 29bp)
GTTGGGCGCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCC728480.4259900974611404RNA PCR Primer, Index 16 (100% over 39bp)
CCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC725200.424072066053727RNA PCR Primer, Index 1 (100% over 33bp)
TGAGAACTGAATTCCATAGATGTGGAATTCTCGGGTGCCAAGGAACTCCA713870.41744667097872873RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA701400.4101546430365198No Hit
TTCAAGTAATCCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA679670.39744768496240573RNA PCR Primer, Index 1 (100% over 28bp)
TGTAACAGCAACTCCATGTGGATGGAATTCTCGGGTGCCAAGGAACTCCA641950.3753903237771512RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG583910.34145052411670124RNA PCR Primer, Index 1 (100% over 29bp)
TGGAGTGTGACAATGGTGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCC558380.32652145648521796RNA PCR Primer, Index 1 (100% over 27bp)
GATCCATGATGACATTAAAACATAACGTGACTGTTGGATGAAGCTTGCGG517570.3026571693704185No Hit
TCTGACACCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCA514650.3009496536052821RNA PCR Primer, Index 16 (100% over 40bp)
TAGCAGCACGTAAATATTGGAGTGGAATTCTCGGGTGCCAAGGAACTCCA510060.2982655791662493RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGC494130.2889502619954883No Hit
TGGACGTGATGAGCAGGTGTTACCGCCCCAGTCTGATGTTTGGTGACTGA486860.28469901555283716No Hit
TGAGGTAGTAGTTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA467050.2731148075708676RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCTGGAATTCTCGGGTGCCAAGGA444210.2597587595997326RNA PCR Primer, Index 1 (100% over 22bp)
ATCCATGATGACATTAAAACATAACGTGACTGTTGGATGAAGCTTGCGGA432110.2526830949565306No Hit
TTCACAGTGGTTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT422240.2469114577641005RNA PCR Primer, Index 1 (100% over 30bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC414580.24243215270898255RNA PCR Primer, Index 1 (100% over 26bp)
TCCCATATGGTCTAGCGGTTAGGATTCCTTGGAATTCTCGGGTGCCAAGG371450.21721120923284182Illumina Small RNA Adapter 2 (100% over 21bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC366800.21449204885342948RNA PCR Primer, Index 1 (100% over 26bp)
GTTCTACAGTCCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC366130.2141002558525249RNA PCR Primer, Index 5 (97% over 35bp)
AATGACACGTTTTCTCCCGGATTTGGAATTCTCGGGTGCCAAGGAACTCC354500.2072994310756291RNA PCR Primer, Index 1 (100% over 27bp)
CTCGTCGCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCA352080.20588429814698866RNA PCR Primer, Index 16 (100% over 40bp)
TCAGTAACTGGAATCTGTCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA350700.2050773215182599RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC348060.20353354014156128RNA PCR Primer, Index 5 (97% over 35bp)
GCCCGGCTAGCTCAGTCGGTAGAGCATGAGACTCTGGAATTCTCGGGTGC324650.18984417573682083No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC321350.18791444901594756No Hit
ATGACCTATGAATTGACAGCCATTGGAATTCTCGGGTGCCAAGGAACTCC315390.18442924560491583RNA PCR Primer, Index 1 (100% over 27bp)
TTCACAGTGGTTAAGTTCTGCCTGGAATTCTCGGGTGCCAAGGAACTCCA311880.18237671809271425RNA PCR Primer, Index 1 (100% over 28bp)
TAACACTGTCTGGTAACGATGTTGGAATTCTCGGGTGCCAAGGAACTCCA311330.18205509697256872RNA PCR Primer, Index 1 (100% over 28bp)
TGAGATGAAGCACTGTAGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT276050.1614245640294144RNA PCR Primer, Index 1 (100% over 30bp)
CTACGCCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCA275010.1608164077295028RNA PCR Primer, Index 1 (100% over 28bp)
CTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC274300.1604012241016786RNA PCR Primer, Index 2 (100% over 34bp)
TTCAGTGATGTTTGACAAATGTCTGACCTGAACTGCAATGTGGACAGATC272590.15940127480086244No Hit
TGAGGTAGTAGGTTGTATAGTTTTGGAATTCTCGGGTGCCAAGGAACTCC258960.1514309186779828RNA PCR Primer, Index 1 (100% over 27bp)
TGCCTGTGATGAGACTCTCGACGGGCGGACTGAATGGGTTTTCACCCTCC256420.14994561386858338No Hit
TTCACAGTGGCTAAGTTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT254290.14870006298511065RNA PCR Primer, Index 1 (100% over 30bp)
ATGACCTATGAATTGACAGCCTTGGAATTCTCGGGTGCCAAGGAACTCCA247200.14455407436359807RNA PCR Primer, Index 1 (100% over 28bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG240180.1404490193391949RNA PCR Primer, Index 1 (100% over 29bp)
TTCACAGTGGCTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG238650.1395543278595173RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGGTTGTATAGTTGGAATTCTCGGGTGCCAAGGAACTCCAG234170.13693457764451358RNA PCR Primer, Index 1 (100% over 29bp)
TTCGGCACCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCA233310.13643167916574053RNA PCR Primer, Index 16 (100% over 40bp)
TGAGGTAGTAGATTGAATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA232360.13587615177639822RNA PCR Primer, Index 1 (100% over 28bp)
ATGACCTATGAATTGACAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT230290.13466568683330501RNA PCR Primer, Index 1 (100% over 30bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCAA227790.13320377265082525No Hit
AGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGT222890.13033842085316494RNA PCR Primer, Index 1 (100% over 30bp)
TTCACAGTGGTTAAGTTCTGCTGGAATTCTCGGGTGCCAAGGAACTCCAG222010.12982382706093204RNA PCR Primer, Index 1 (100% over 29bp)
CCGTCGAGCAGCATTCCGGGCTTCACATCGGAGGGCTCCAGCCGGCCCCG221580.12957237782154554No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA218840.12797011987754772RNA PCR Primer, Index 1 (100% over 28bp)
CATTGCACTTGTCTCGGTCTGATGGAATTCTCGGGTGCCAAGGAACTCCA218230.12761341281702268RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAAATCCAGTCACCCGTCCATCTCGTATGC215650.12610471738070356RNA PCR Primer, Index 16 (98% over 50bp)
TATTGCACTTGTCCCGGCCTGTTTGGAATTCTCGGGTGCCAAGGAACTCC214890.12566029546922972RNA PCR Primer, Index 1 (100% over 27bp)
TGAGAACTGAATTCCATAGATGGTTGGAATTCTCGGGTGCCAAGGAACTC213730.1249819672885591RNA PCR Primer, Index 1 (100% over 26bp)
TAACGGAACCCATAATGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA210680.12319843198593382RNA PCR Primer, Index 1 (100% over 28bp)
ACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCG205100.119935439530639RNA PCR Primer, Index 7 (97% over 36bp)
TGTAACAGCAACTCCATGTGGAATGGAATTCTCGGGTGCCAAGGAACTCC202140.11820453313858297RNA PCR Primer, Index 1 (100% over 27bp)
AGAGATGATGACTTCTGTTACCGCCCCAGTCTGAGAAGTCATGACTGATC190480.11138616539149741No Hit
TTCAAGTAATCCAGGATAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGT185380.10840386045923871RNA PCR Primer, Index 1 (100% over 30bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC185330.1083746221755891No Hit
TCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCC184130.10767290336799883No Hit
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGCC182980.10700042284405814No Hit
TAACACTGTCTGGTAACGATGTGGAATTCTCGGGTGCCAAGGAACTCCAG182950.10698287987386838RNA PCR Primer, Index 1 (100% over 29bp)
TGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCC181500.10613496964803013RNA PCR Primer, Index 5 (97% over 35bp)
GTAACGGAACCCATAATGCAGCTTGGAATTCTCGGGTGCCAAGGAACTCC179940.10522273519816276RNA PCR Primer, Index 1 (100% over 27bp)
GGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC178720.10450932107711264RNA PCR Primer, Index 2 (100% over 34bp)
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTGCTGGAATTCTCGGGTGCC175440.1025912896696992No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA175170.10243340293799139No Hit
CTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC173590.10150947317466419RNA PCR Primer, Index 2 (100% over 34bp)
TGGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC172180.1006849535757456RNA PCR Primer, Index 1 (100% over 33bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGTGGAATTCTCGGGTGCCAAGGA172150.10066741060555584RNA PCR Primer, Index 1 (100% over 22bp)
AATGACACGTTTTCTCCCGGATTGTGGAATTCTCGGGTGCCAAGGAACTC172110.10064401997863616RNA PCR Primer, Index 1 (100% over 26bp)
CGGGCCACCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCCGTCCA171250.10014112149986314RNA PCR Primer, Index 16 (100% over 40bp)

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CCCACGC454.802132E-1043.9994834
ACGTACC454.802132E-1043.9967824
ATGCGAC22350.043.99677726
GATAATC351.4490251E-743.9947214
ATCTATA2000.043.9947210
GTATCTA1950.043.994728
CTAGGTA600.043.99317616
GTACAAG850.043.993053
CGTTGCG351.4494617E-743.993056
ACGATTA1050.043.993057
GCTATCC207.8656693E-443.9930467
CTACGAA207.8656693E-443.9930466
CTTTCTA302.532539E-643.9930466
AACATTC249150.043.9070931
TGACCTA1199000.043.8597262
TAGCTTA679050.043.8580671
TTCAACG224450.043.8558465
CTATGAA1199900.043.846396
ACCTATG1199900.043.846394
TAACACT60350.043.820741