FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n02_female_transmission_spinal_cord_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n02_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
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC79451.189184334797674No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC16910.2531039282747472No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC16810.25160715755756957No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA15750.23574138795548605No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA15540.2325981694494129No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC15370.23005365923021082No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT15280.22870656558475091No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA13590.20341114046444797No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG12990.19443051616138182No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG12510.1872460167189289No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGATAGAGTCATCT12430.18604860014518676No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC12020.17991184020475823No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA11880.17781636120070946No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC11710.17527185098150738No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA11640.17422411147948302No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC11630.17407443440776524No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC11200.1676383203239012No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC10630.15910672723598837No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGGCTGTTTCCAGTGACTTCCGC10570.15820866480568174No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC10560.15805898773396398No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA10470.15671189408850406No Hit
GTGCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCACAGATGGCCAT10440.15626286287335076No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT10350.15491576922789083No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC10260.1535686755824309No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG10070.15072481121979328No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC9810.1468332073551313No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT9790.14653385321169576No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA9760.14608482199654246No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT9630.14413902006421145No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG9530.1426422493470338No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC9110.1363558123348875No Hit
GTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCCAGACGGGAAG9020.13500871868942757No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG8910.1333622709005321No Hit
CTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTG8780.1314164689682011No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC8770.13126679189648333No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG8730.13066808360961227No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC8550.1279738963186924No Hit
TCTTCTGTCTGTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCC8490.1270758338883858No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG8390.12557906317120812No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG8290.12408229245403042No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT8230.12318423002372382No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG8190.12258552173685273No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA8090.12108875101967505No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT8000.11974165737421512No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG7810.11689779301157753No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC7780.11644876179642422No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG7680.11495199107924652No Hit
CTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTGCGAGTCATCACTCTG7670.11480231400752874No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC7660.11465263693581097No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA7650.11450295986409323No Hit
GATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGA7610.11390425157722214No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC7580.11345522036206883No Hit
GTATGGATCAAGTCTTCCCTCACCGCTCCTCAGTGCGGCTCCTTTTGTAA7580.11345522036206883No Hit
GTGTTAGAGCAGCCAAGATTGGTAGAGCGATGTTGTCAGTGCGTGGCACG7530.11270683500348No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG7510.11240748086004446No Hit
GGTTTGTTAGGGTTCCTGCCTATACGTCCTCTCCTCTGAGCAGCACTAGC7490.11210812671660891No Hit
GGCTGGACCCATGGCTGCAGTAGGCTTGCTAATTGTTAGCTATGTGGTCT7460.11165909550145561No Hit
TGCTAATTGTTAGCTATGTGGTCTCGGGAAAGAGTGTGGACATGTACATT7460.11165909550145561No Hit
GGAGCATGATCCCTCCACAAGTAGCCAGGCCCGCTCTCCATGCCACGAGC7450.11150941842973784No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC7440.11135974135802007No Hit
GCACGCGCTGCTGCCGCTTGTAGGCCTGGGATCAAGTACATGTAGTGCGC7390.11061135599943124No Hit
CTTGTGGAGGGATCATGCTCCTCTCCCTGAAAGGGAAAGGTAGTGTGAAG7370.1103120018559957No Hit
GCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGG7250.10851587699538245No Hit
GGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGGGGTCA7220.10806684578022917No Hit
ACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCCAG7190.10761781456507585No Hit
GAGTATGATCTCTCTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAAT7180.10746813749335808No Hit
ATGTTAGTGCTATAACCCAGGGAAAGAGGGAGGAGGAGACTCCGGTTGAA7060.10567201263274484No Hit
GCCTTATAAGGCCTGCTTCCAGTCTCTGCTCGCATGAGCACGGCGAGGTT7050.1055223355610271No Hit
CTCTAACACCACTAGCTCGAGGCACACTGCTCGTGGCATGGAGAGCGGGC6950.1040255648438494No Hit
GGTATAGCTATTGGGTTCATGCCACAGATGGCCATCAGGACCACCTTGAG6930.10372621070041385No Hit
AACTTACACAGACAGAAGATGGTGCTTTGATGGCACAACCAACAACACCA6900.10327717948526054No Hit
GTACATGTCCACACTCTTTCCCGAGACCACATAGCTAACAATTAGCAAGC6840.10237911705495394No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC6830.10222943998323616No Hit
GGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCT6790.1016307316963651No Hit
TCCTGAAATAGTCCGTGAAGCCATAAAAAAGAGACTCCGGACAGTGATCT6760.10118170048121179No Hit
CCTCGCTGAGTCCATCCCAAGCTGCATCCAACTTCCAAGGCCCACAGTAT6700.10028363805090518No Hit
GGGTTATAGCACTAACATAGCTTCCATTCTTGATCACAACCCCATTGCCA6690.1001339609791874No Hit
GTTGTAGTAAGCGTGAAGTGAAAGTGGCATGGCACATCAAATCAACGATT6690.1001339609791874No Hit

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GCTTAGC100.00724006143.990051
GACGTTA100.0072465437143.946959
AGATAAG2600.096.9163741
GCCTGCA1800.091.9867553
CCTGTTA451.23603E-463.9907844
CTGCGCG451.2374042E-463.976419
GAGATAA808.540155E-962.9956441
CTGTTAT350.00366718761.70545
ACTGGAG20350.060.1387633
TGGAGAT21300.058.8084345
CTGGAGA21150.058.204384
CTGTGCC1750.057.5917053
GCCTGTT651.1399645E-555.376643
TCTGTGC1900.053.044992
CCCAGGA6000.041.9845289
CCTGCGC700.001094956241.1276978
GGAGATG42200.035.1418576
TACTACA8500.033.880011
CTACAAC8650.033.2900053
ACTACAA8700.033.098682
Produced by FastQC (version 0.11.2)