FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_female_transmission_brain_pcr1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_female_transmission_brain_pcr1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences439785
Sequences flagged as poor quality0
Sequence length150
%GC50

[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

[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

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GAATGGTTTTGGCGATACTAGCCTTTTTGAGATTTACAGCAATCAAGCCA22190.5045647304933092No Hit
GTATTACCTGACCATGAACAATAAGCATTGGTTGGTGCACAAAGAGTGGT12510.28445717793922026No Hit
CTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTA12050.27399752151619544No Hit
GTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCAGGCAATGGCAA11210.25489727935241085No Hit
ATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGCAACAC11050.25125913798788047No Hit
GGTAATACAGATCTGAAAAGTCAAGGCCTGTCCTTGGTTCACAGTCAAGT10810.24580192594108483No Hit
GAGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCG9300.21146696681332922No Hit
TCCTTGTAGAGTGAGAAGGGAGCGTCACGGCTCTTCTAGATCGCCGTGCC8890.20214422956672007No Hit
GAATATGACACGCCCTTCAATCTAAGCTTGTCCATTTTTAGGCGGCATTT8770.19941562354332232No Hit
ATCTAAGCTTGTCCATTTTTAGGCGGCATTTCAAATGGCCAGAGAACAGC8240.18736428027331536No Hit
GTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGCATAGGAGTGG7960.18099753288538717No Hit
TCCGTACACAACCCAAGTTGATGTCGTGTTGCACCAGCAATCGACATCAT7660.17417601782689268No Hit
TTCATATCCTGTATCATTGACAATCATCCCGCTATGCTGGGAGCCATGCA7550.17167479563877805No Hit
AGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGGATTTG7490.17031049262707915No Hit
CATATTGAGTGTCTGATTGCTTGTCAAGGTAGGCTTCACCTTGTGTTGGG7180.1632615937333015No Hit
CTTCTAGATCGCCGTGCCTCACCTTTTTTGTGATGACAGGTTCCGTACAC7170.16303420989801837No Hit
GTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAAATCC7100.1614425230510363No Hit
GTCATGGACCCATCAGAATGGTTTTGGCGATACTAGCCTTTTTGAGATTT6820.15507577566310812No Hit
GTTAGTAACATGGCCGAGGTAAGATCCTATTGCTACGAGGCATCGATATC6780.1541662403219755No Hit
CTCAATATGTCTGCAAAAGAACATTAGTGGACAGAGGTTGGGGAAACGGT6740.15325670498084293No Hit
TCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAAA6640.15098286662801141No Hit
GTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGTATCAG6570.14939117978102937No Hit
CTCCAAGAGAGAAGTGGTCCATATGATCGGTTGACCCCGCTGTCACCATT6570.14939117978102937No Hit
CCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGA6530.14848164443989675No Hit
GTCATATTCCTTGTGCACTGCGGCATTCACATTCACCAAGGTCCCAGCTG6530.14848164443989675No Hit
ACTCTATGTCAACTGTTGGCTTGTCCTGTGCCATCACGGTAACGCAGCCT6520.1482542606046136No Hit
GTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTGTAGTCA6520.1482542606046136No Hit
GTACAGATCATGGACCTCGGGCACATGTGTGACGCCACCATGAGTTATGA6500.14779949293404732No Hit
TCTTAGAACACGTAAACTTGGCACATGTCACCAAGCTCCCTTTGCCAAAA6500.14779949293404732No Hit
TAATAAAGAAGTTCAAGAAAGATCTTGCTGCCATGTTGAGAATAATCAAT6430.14620780608706527No Hit
GTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAGAGGGTTACAGAA6310.1434792000636675No Hit
AGCTTAGATTGAAGGGCGTGTCATATTCCTTGTGCACTGCGGCATTCACA6240.14188751321668544No Hit
CTACAAGGAAGTTGCAAACGCGGTCGCAGACCTGGTTAGAATCAAGAGAA6240.14188751321668544No Hit
ATCTAGAAGAGCCGTGACGCTCCCTTCTCACTCTACAAGGAAGTTGCAAA6190.14075059404026968No Hit
CTCATAACTCATGGTGGCGTCACACATGTGCCCGAGGTCCATGATCTGTA6020.13688506884045612No Hit
GCATACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTT5960.13552076582875724No Hit
GTTCGAGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGG5930.13483861432290778No Hit
CTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTTTTG5910.1343838466523415No Hit
GTACAAGTACCATCCTGACTCCCCCCGCAGATTGGCAGCAGCAGTCAAGC5870.1334743113112089No Hit
TCCCTTAACAGCTGTTCCTATGACGGCTGGGTCACATTCTAATGAGTAAT5780.13142785679366054No Hit
ATCCAGCATAGGGCACTCATAACTCATGGTGGCGTCACACATGTGCCCGA5720.13006355378196163No Hit
GATCTGTACGTGGCACTTGTTCACTCCCAATGTGGTAGCAAACGAAATGG5710.1298361699466785No Hit
ATCATGACCAAGTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCA5670.12892663460554588No Hit
TTCTTACATTGTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGC5670.12892663460554588No Hit
GGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATTGGGAG5600.12733494775856383No Hit
TACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGC5570.1266527962527144No Hit
GTATCAGGTGCATTGGAGTCAGCAATAGAGACTTCGTGGAGGGCATGTCA5430.1234694225587503No Hit
ACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTG5390.12255988721761771No Hit
ACCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATG5380.12233250338233455No Hit
GTACATGTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTG5320.12096820037063566No Hit
ATCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAA5250.1193765135236536No Hit
GGATATGAAACTGACGAAAATAGAGCGAAAGTCGAGGTTACGCCTAATTC5210.118466978182521No Hit
CACTAGCAGCGTGCCTATGAGGATCTGTGAGAACCAGGACATTCCTCCAA5170.1175574428413884No Hit
GTTGAGAATAATCAATGCTAGGAAAGAGAGGAAGAGACGTGGCGCAGACA5160.11733005900610524No Hit
GTTACTAACCGTCGTCGTGACCAACTCTATGTCAACTGTTGGCTTGTCCT5150.1171026751708221No Hit
TTCCTTCAGTGTGTCACCGTCGACAACAAAACTGTTGTTGGTCTTTGCCG5120.11642052366497264No Hit
ATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTT5110.1161931398296895No Hit
GTATCAACAGGTTTAATTTGGATTTGGAAACGAGAGTTTCTGGTCATGAA5100.11596575599440635No Hit
TCCATGCTCTGTGCTCAAGCGGACATTCCTTCAGTGTGTCACCGTCGACA5080.11551098832384007No Hit
TTCCAAGACAACATCAACCCAGGTCCCACCTGACATGCCCTCCACGAAGT5070.11528360448855692No Hit
GGGTAAGGGCATTCACCAGATTTTTGGAGCAGCCTTCAAATCACTGTTTG5050.11482883681799062No Hit
TACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATT5050.11482883681799062No Hit
GGCCTGGGAAGAGGGGATCTGTGGGATCTCATCCGTTTCAAGAATGGAAA5030.11437406914742432No Hit
GCTAAAGACTTGGGTATGATAAGATCACTTTCTTCTACTCCATCTGTCCA5000.11369191764157487No Hit
ATATCGGACATGGCTTCGGACAGTCGTTGCCCAACACAAGGTGAAGCCTA4990.11346453380629172No Hit
AGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGA4960.11278238230044227No Hit
GTCAGTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAA4940.11232761462987596No Hit
TTATAGATGAATACCCCCGTGCCACATCTCGTTTCCTTTTTTGAGAAGTC4940.11232761462987596No Hit
GTCTCACACATTGTGGACAGATGGAGTAGAAGAAAGTGATCTTATCATAC4890.11119069545346022No Hit
TCTCACAGTGGCCTCAAATGCCTTTCCGATGGTGCTACCACTCCTATGCC4790.1089168571006287No Hit
TCTATAATGATGTTGAAGCCTGGAGGGACCGGTACAAGTACCATCCTGAC4760.10823470559477927No Hit
CATTGGGAGTGAACAAGTGCCACGTACAGATCATGGACCTCGGGCACATG4690.1066430187477972No Hit
GCATACTGCACCTCCACTGTGACTGTTCCATGCAGTGTTTCAGCTGGGAC4690.1066430187477972No Hit
ATTCTAACCAGGTCTGCGACCGCGTTTGCAACTTCCTTGTAGAGTGAGAA4660.10596086724194775No Hit
CTCACGGGGTGTCCAATTGGCTCTGAAAATGAAGGAGACCAGCAAGGCTG4590.10436918039496573No Hit
CTCCTATGCCAGTGGTGGGTGATTTTCTTGTCCCCAACTCCTATGACAAT4580.10414179655968259No Hit
ACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACC4580.10414179655968259No Hit
ATGTAAGAATCCCCAAATGGTGGGTCAAGCTCCAACATCATCTTTGAGTT4580.10414179655968259No Hit
TCCCAGGCCTGCTTGACTGCTGCTGCCAATCTGCGGGGGGAGTCAGGATG4540.10323226121854998No Hit
TATCATACCCAAGTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAG4540.10323226121854998No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG4510.10255010971270052No Hit
TCCTTGAATTCTACCAATGCCTCTTTGTTGTTCCAGTGTGGAGTTCCGGT4460.10141319053628478No Hit
CCTCTAGGATAGCATTGAGCTCCCCTTCTACTGATTTCCACATGATGTTT4440.10095842286571848No Hit
GCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGC4420.10050365519515217No Hit

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TTTAATG100.007238189143.996934
TAATGCC100.007238189143.996936
TGCGTGG2200.078.5437852
AGTTCGA651.6498234E-977.536812
GTGCGTG2250.076.80711
CAGTGCG1000.071.998473
GTCAGTG1050.068.577771
CAGTTCG755.114998E-967.206211
GCGTGGC2650.065.2061543
CGAGTCT1001.0913936E-1164.798624
AGTGCGT1150.062.6073654
GTTCGAG1051.6370905E-1161.719991
TCGAGTC1051.6370905E-1161.712973
TTCGAGT1102.7284841E-1158.907842
AGTCTGA1850.054.4915241
AGATAAA400.006214243454.004991
GATAAAA400.006217039753.9988482
GTCTGAA1950.051.6912082
CACGGCC3400.050.8224459
TGAAGCG2000.050.3989265
Produced by FastQC (version 0.11.2)