FastQCFastQC Report
Mon 5 Dec 2016
JM83_3_GTGGCC_L008_R1_001.fastq

Summary

[OK]Basic Statistics

MeasureValue
FilenameJM83_3_GTGGCC_L008_R1_001.fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences15193692
Sequences flagged as poor quality0
Sequence length50
%GC57

[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
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTATGC416827027.43421414623911RNA PCR Primer, Index 20 (100% over 50bp)
TCAGTAACTGGAATCTGTCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA1544291.0164020700169518RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA1339230.8814381652596354RNA PCR Primer, Index 1 (100% over 28bp)
GTCTTTGCTGCGAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG1150390.7571497434593251RNA PCR Primer, Index 6 (100% over 34bp)
TGGAGTGTGACAATGGTGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCA1073260.7063852551440427RNA PCR Primer, Index 1 (100% over 28bp)
ATGACCTATGAATTGACAGCCATGGAATTCTCGGGTGCCAAGGAACTCCA875520.5762391392427858RNA PCR Primer, Index 1 (100% over 28bp)
ATGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG860740.5665114180279553RNA PCR Primer, Index 1 (100% over 29bp)
GGTGTCCGACGCCGGGTGGATGGCTGGAATTCTCGGGTGCCAAGGAACTC771460.5077501900130659RNA PCR Primer, Index 1 (100% over 26bp)
AAGCTGCCAGCTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA704930.4639622811887986RNA PCR Primer, Index 1 (100% over 28bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA628120.4134084065939997RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGCTGGAATTCTCGGGTGCCAAGGAACTCC617090.4061488149160849RNA PCR Primer, Index 1 (100% over 27bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTGGCCATCTCGTAT594240.39110967893781184RNA PCR Primer, Index 20 (100% over 48bp)
TCAGTAACTGGAATCTGTCCCTGTGGAATTCTCGGGTGCCAAGGAACTCC573840.37768305425699034RNA PCR Primer, Index 1 (100% over 27bp)
CGCCTGCCCGGTGTCGCTCGGGTGGAATTCTCGGGTGCCAAGGAACTCCA523450.34451797495960823RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA482550.31759890881031416RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG465300.3062455129405019RNA PCR Primer, Index 1 (100% over 29bp)
TGGAGTGTGACAATGGTGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCC439680.2893832519442937RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA434250.28580940037483976RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC416280.2739821236339397RNA PCR Primer, Index 1 (100% over 33bp)
GCGCCTCGCGCGTCGGCGGGCGGTGGGATGGAATTCTCGGGTGCCAAGGA415390.273396354223845RNA PCR Primer, Index 1 (100% over 22bp)
ACTGTATAAGGTACATATGGTTGAGTGTCGTATGGAATTCTCGGGTGCCA412470.2714745040244333No Hit
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT389310.25623133600444187RNA PCR Primer, Index 1 (97% over 35bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA373750.2459902438459329No Hit
GTTCTACAGTCCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGT361220.23774340035325187RNA PCR Primer, Index 1 (97% over 35bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG359770.23678905693231114RNA PCR Primer, Index 1 (100% over 29bp)
GGTGTCCGACGCCGGGTGGATTGGAATTCTCGGGTGCCAAGGAACTCCAG306730.20187983276217528RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC299220.19693699200957873RNA PCR Primer, Index 1 (100% over 27bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA284770.1874264661939968RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGG281960.1855770144610013No Hit
TTCAAGTAATCCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA271040.17838982124950276RNA PCR Primer, Index 1 (100% over 28bp)
CTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG260900.17171599898168266RNA PCR Primer, Index 6 (100% over 34bp)
CGCCCGGGCGGGGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG259880.1710446677476416RNA PCR Primer, Index 6 (100% over 34bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC259690.17091961585110452No Hit
CGCCTCGCGCGTCGGCGGGCGGTGGGATGGAATTCTCGGGTGCCAAGGAA245450.1615473052895899RNA PCR Primer, Index 1 (100% over 23bp)
GCCGCCCGGGCGGGGACCGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC237700.15644650424663079RNA PCR Primer, Index 1 (100% over 31bp)
GGCAGGTCAGGGACGGCCGCTCGGCGCGGGATGGAATTCTCGGGTGCCAA237230.15613716534467068No Hit
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG227140.14949625147067613RNA PCR Primer, Index 6 (100% over 34bp)
TAACGGAACCCATAATGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC223740.1472584806905392RNA PCR Primer, Index 1 (100% over 27bp)
TGGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC223160.1468767433221629RNA PCR Primer, Index 1 (100% over 33bp)
CCCTCCTCGTGGGGGGGGCGGGGGACTTGGAATTCTCGGGTGCCAAGGAA219810.14467188093585154RNA PCR Primer, Index 1 (100% over 23bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTTGGAATTCTCGGGTGCC218270.1436583024060248No Hit
GGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG217000.14282242920285604RNA PCR Primer, Index 6 (100% over 34bp)
CTGTCGACCGGAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTG213950.14081501717949793RNA PCR Primer, Index 15 (97% over 36bp)
CGTGGTGGGGCCCCCTTCGTCCGTCTGGAATTCTCGGGTGCCAAGGAACT211070.13891949369514664RNA PCR Primer, Index 1 (100% over 25bp)
TCAGTAACTGGAATCTGTCCCTGCTGGAATTCTCGGGTGCCAAGGAACTC202960.1335817522166436RNA PCR Primer, Index 1 (100% over 26bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA188000.12373556078404116No Hit
TAGCTTATCAGACTGGTGTTGGTGGAATTCTCGGGTGCCAAGGAACTCCA186930.12303132115617456RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAGGAACTCCAGTCACGTGGCCATCTCGTATGCC186000.12241922503101944RNA PCR Primer, Index 20 (97% over 35bp)
CCCTCCTCGTGGGGGGGGCGGGGGACTGGGCTGGAATTCTCGGGTGCCAA184370.12134641139230676No Hit
TCCCATATGGTCTAGCGGTTAGGATTCCTTGGAATTCTCGGGTGCCAAGG182680.1202341076810034Illumina Small RNA Adapter 2 (100% over 21bp)
TCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC181680.11957593980449256RNA PCR Primer, Index 1 (100% over 33bp)
GGACAACTCTTAGCGGTGGATCTGGAATTCTCGGGTGCCAAGGAACTCCA176420.11611397677404543RNA PCR Primer, Index 1 (100% over 28bp)
AGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGT170230.11203991761844323RNA PCR Primer, Index 1 (100% over 30bp)
CGCGCCGCCCGGGCGGGGACCGTGGAATTCTCGGGTGCCAAGGAACTCCA166280.10944015450622534RNA PCR Primer, Index 1 (100% over 28bp)
GATGCGGTCGGCGGGTGCGGCGGCGACTGGAATTCTCGGGTGCCAAGGAA165110.10867009809070764RNA PCR Primer, Index 1 (100% over 23bp)
TGAGGTAGTAGTTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA162570.10699835168437007RNA PCR Primer, Index 1 (100% over 28bp)
AGCCTGTGATGATACAAGTTATCCCTGTCTGAACTCTGGTGTGGAATTCT162200.10675482957006105No Hit
TGAGAACTGAATTCCATAGATGGTGGAATTCTCGGGTGCCAAGGAACTCC161410.10623487694761746RNA PCR Primer, Index 1 (100% over 27bp)
AACTCTTAGCGGTGGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA159970.10528711520544184RNA PCR Primer, Index 1 (100% over 32bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC158300.10418797485166871RNA PCR Primer, Index 1 (100% over 26bp)
ACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGTG158000.10399052448871544RNA PCR Primer, Index 15 (97% over 36bp)
TAACACTGTCTGGTAACGATGTTGGAATTCTCGGGTGCCAAGGAACTCCA154980.10200285750165267RNA PCR Primer, Index 1 (100% over 28bp)

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CTTCACG207.821309E-444.043571
CGTTCTA207.821309E-444.043571
TACTTAA1500.044.0435641
GTATCAT454.802132E-1044.0015318
CTATAGG750.044.00138512
ATATTAG551.8189894E-1244.00138514
TTATAGG900.044.00109515
AGTTTCC207.862252E-443.996933
ATAACTA2150.043.996922
CCTAGCC207.8623794E-443.99675432
GATATGT502.7284841E-1143.9967542
GTGTACG207.8623794E-443.9967542
CGATAAT254.447355E-543.99675420
CACTAGG750.043.9967531
CGGGCTA207.8626344E-443.99646425
CTCATCG302.5311674E-643.9964648
ATCGCAA302.5311674E-643.99646425
ATCTATA750.043.9964610
TCTATGC454.802132E-1043.996469
ATATGTT502.7284841E-1143.9961743