FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_female_transmission_spinal_cord_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_female_transmission_spinal_cord_pcr2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences668105
Sequences flagged as poor quality0
Sequence length150
%GC51

[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

[OK]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
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC86581.2959040869324432No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA18430.2758548431758481No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC17940.2685206666616774No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC17040.2550497302070782No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA16750.2507090951272629No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT16550.24771555369290754No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA15150.22676076365241987No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA15000.22451560757665334No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC14690.21987561835340252No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGATAGAGTCATCT14100.2110446711220542No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA13680.20475823410990787No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG13420.2008666302452459No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG13150.1968253493088661No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC13070.195627932735124No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC13060.1954782556634062No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA12990.19443051616138182No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC12860.19248471422905084No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC12470.18664730843205782No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC12050.18036087141991153No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGGCTGTTTCCAGTGACTTCCGC11660.17452346562291857No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC11210.16778799739561895No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG11190.1674886432521834No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT11040.16524348717641688No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC10920.16344736231580365No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT10780.1613518833117549No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC10420.1559635087299152No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA10410.15581383165819743No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG10270.15371835265414868No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT10120.15147319657838215No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC9880.1478809468571557No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG9770.14623449906826022No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG9750.14593514492482468No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG9730.14563579078138914No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG9500.14219321813188046No Hit
GTGCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCACAGATGGCCAT9290.1390499996258073No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA9220.13800226012378294No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG9120.13650548940660523No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG9090.13605645819145196No Hit
GTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCCAGACGGGAAG9090.13605645819145196No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC8910.1333622709005321No Hit
CTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTG8800.13171582311163665No Hit
CTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTGCGAGTCATCACTCTG8680.12991969825102342No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC8670.12977002117930567No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG8600.12872228167728125No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC8600.12872228167728125No Hit
GCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGG8500.1272255109601036No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC8290.12408229245403042No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC8140.1218371363782639No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC8120.12153778223482836No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT8090.12108875101967505No Hit
CTCTAACACCACTAGCTCGAGGCACACTGCTCGTGGCATGGAGAGCGGGC8070.12078939687623952No Hit
ACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCCAG8070.12078939687623952No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA8060.12063971980452175No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT8000.11974165737421512No Hit
AACTTACACAGACAGAAGATGGTGCTTTGATGGCACAACCAACAACACCA7820.1170474700832953No Hit
CTTGTGGAGGGATCATGCTCCTCTCCCTGAAAGGGAAAGGTAGTGTGAAG7800.11674811593985976No Hit
TCTTCTGTCTGTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCC7670.11480231400752874No Hit
GTTGTAGTAAGCGTGAAGTGAAAGTGGCATGGCACATCAAATCAACGATT7640.11435328279237546No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC7630.11420360572065769No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG7620.11405392864893991No Hit
GGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGGGGTCA7580.11345522036206883No Hit
GATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGA7480.11195844964489116No Hit
GTATGGATCAAGTCTTCCCTCACCGCTCCTCAGTGCGGCTCCTTTTGTAA7440.11135974135802007No Hit
GGCTGGACCCATGGCTGCAGTAGGCTTGCTAATTGTTAGCTATGTGGTCT7280.10896490821053577No Hit
ATACTGGGGGGATGTCAAGCAGGACTTGGTGTCATACTGTGGGCCTTGGA7250.10851587699538245No Hit
GTGTTAGAGCAGCCAAGATTGGTAGAGCGATGTTGTCAGTGCGTGGCACG7210.1079171687085114No Hit
CTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAATCACCACTCTCATC7140.10686942920648701No Hit
CACATACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCA7140.10686942920648701No Hit
TGCTAATTGTTAGCTATGTGGTCTCGGGAAAGAGTGTGGACATGTACATT7100.10627072091961592No Hit
GGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCT7090.10612104384789815No Hit
CATCAATGGCAGTGCTGGTAGTCATGATCTTGGGAGGATTTTCAATGAGT7080.10597136677618038No Hit
GCCTTATAAGGCCTGCTTCCAGTCTCTGCTCGCATGAGCACGGCGAGGTT7070.10582168970446261No Hit
GGAGTGTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGG7070.10582168970446261No Hit
GCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAACCTGGAGATGA7030.10522298141759155No Hit
TCCCAGAGGGCGCCACTCCTTTTCCCAGTCTTCACATACACATACCACGC7020.10507330434587378No Hit
ATGTTAGTGCTATAACCCAGGGAAAGAGGGAGGAGGAGACTCCGGTTGAA7010.10492362727415601No Hit
CCCACCTCCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTA6930.10372621070041385No Hit
TCCTGAAATAGTCCGTGAAGCCATAAAAAAGAGACTCCGGACAGTGATCT6830.10222943998323616No Hit
ATCATACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGC6830.10222943998323616No Hit
GAGTATGATCTCTCTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAAT6820.10207976291151839No Hit
GCTCATACCCGAGCCAGAGAAGCAAAGATCTCCCCAAGATAACCAGATGG6760.10118170048121179No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CCTGTTA351.9954314E-9123.426974
GCCTGTT351.9954314E-9123.426973
GCCTGCA1800.0111.998543
AGATAAG2400.096.02751
GAGATAA651.6370905E-1188.640771
TCAGAAT259.635992E-486.424751
CTGTTAT502.3792381E-886.398875
ACTGGAG24750.067.780943
CTGGAGA25950.064.646564
TGGAGAT26000.064.522245
TCTGTGC1051.6370905E-1161.7134862
CAGAATC400.006218241553.9993022
TGTTATT806.1585706E-753.9993026
AACAGGC1101.7753337E-952.3786351
CCCAGGA4900.044.081069
CTGTGCC1755.638867E-1141.1423233
GGAGATG47800.039.91586
TACTACA8200.037.766911
ACTACAA8250.037.5267832
GCACAGA1752.5975169E-937.028096
Produced by FastQC (version 0.11.2)