FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_female_transmission_brain_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_female_transmission_brain_pcr2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences531255
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

[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

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC55201.0390490442442895No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA14790.2783973797893667No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC14680.2763268110417784No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT13380.2518564531157354No Hit
GTGCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCACAGATGGCCAT12750.23999774119772993No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG11910.22418612530705592No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA11760.22136262246943558No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC11580.21797441906429116No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC11100.20893920998390605No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA10670.20084516851606102No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA10600.19952753385850489No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA10350.19482169579580427No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC9970.1876688219404994No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC9900.18635118728294323No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG9600.18070418160770252No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGGCTGTTTCCAGTGACTTCCGC9500.17882184638262227No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC9400.17693951115754206No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA9390.17675127763503404No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC9390.17675127763503404No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG9050.17035133786976123No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG9040.1701631043472532No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGATAGAGTCATCT8970.16884546968969702No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC8320.1566102907266755No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT7950.14964565039387864No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC7920.14908094982635456No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT7880.14832801573632248No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC7780.14644568051124227No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT7680.14456334528616202No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC7540.14192807597104967No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC7450.14023397426847747No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG7250.136469303818317No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC7230.13609283677330095No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA7110.13383403450320466No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC7050.13270463336815655No Hit
GCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGG7010.13195169927812445No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA7010.13195169927812445No Hit
ACTTAGTGAGGTCAATGGTGACAGCGGGGTCAACCGATCATATGGACCAC6910.13006936405304423No Hit
GTGTTAGAGCAGCCAAGATTGGTAGAGCGATGTTGTCAGTGCGTGGCACG6870.12931642996301213No Hit
CTCTAACACCACTAGCTCGAGGCACACTGCTCGTGGCATGGAGAGCGGGC6850.12893996291799606No Hit
CATCAATGGCAGTGCTGGTAGTCATGATCTTGGGAGGATTTTCAATGAGT6690.1259282265578677No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG6670.12555175951285164No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT6580.12385765781027942No Hit
CTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTG6580.12385765781027942No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC6570.1236694242877714No Hit
GATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGA6550.12329295724275537No Hit
CTCCCACTCCAACCTGTGTTGAACCTAGCAGTCTGCGAGTCATCACTCTG6550.12329295724275537No Hit
CTTGTGGAGGGATCATGCTCCTCTCCCTGAAAGGGAAAGGTAGTGTGAAG6540.12310472372024735No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC6500.12235178963021524No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG6490.12216355610770721No Hit
CTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAATCACCACTCTCATC6410.12065768792764303No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG6410.12065768792764303No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC6230.11726948452249861No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG6180.1163283169099585No Hit
GGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGGGGTCA6140.1155753828199264No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG6070.11425774816237023No Hit
TTTAAAGTCAGACCAGCCTTGCTGGTCTCCTTCATTTTCAGAGCCAATTG6050.11388128111735418No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA5970.11237541293729No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG5970.11237541293729No Hit
GTACATGTCCACACTCTTTCCCGAGACCACATAGCTAACAATTAGCAAGC5900.11105777827973384No Hit
CCATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTG5900.11105777827973384No Hit
GGCTGGACCCATGGCTGCAGTAGGCTTGCTAATTGTTAGCTATGTGGTCT5890.11086954475722581No Hit
ACCTTTCCCTTTCAGGGAGAGGAGCATGATCCCTCCACAAGTAGCCAGGC5790.10898720953214558No Hit
TGCTAATTGTTAGCTATGTGGTCTCGGGAAAGAGTGTGGACATGTACATT5680.10691664078455732No Hit
GAGTATGATCTCTCTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAAT5640.10616370669452524No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG5620.10578723964950919No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC5590.1052225390819851No Hit
GCTATTGGGTTCATGCCACAGATGGCCATCAGGACCACCTTGAGTATGAT5550.10446960499195303No Hit
GGCCAAGCTTGTGATCCTGATGGGTGCTACTTTCGCAGAAATGAACACTG5490.10334020385690487No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC5450.10258726976687278No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT5440.10239903624436476No Hit
GCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGCCACGCACTGACAA5390.10145786863182465No Hit
ATTGGACACCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTG5360.10089316806430057No Hit
CCCTGAAAGGGAAAGGTAGTGTGAAGAAGAACCTGCCATTTGTCATGGCC5330.1003284674967765No Hit

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GCCTGTA502.055458E-10100.7969063
GCCTGCA2650.097.808313
GATGGTA301.6549122E-595.997059
AGATAAG2550.093.1911541
GAGATAA1100.078.557831
GCGTCAG300.001987861572.0113451
CGTCAGA300.001989346771.997782
TCTGTGC2900.069.515112
CTGGAGA17450.067.2529454
TGGAGAT17850.065.745885
CCTGTCC451.235105E-463.998038
ACTGGAG20000.058.67823
ATTTAGC400.006217980353.998349
GTATTTA400.006217980353.998347
TACCTCT400.006217980353.998344
TGCAAGG400.006217980353.998342
CTGTGCC3800.053.0510033
CTGTATT450.00990494947.9985245
AGATGTG450.00990494947.9985246
CCCAGGA4850.047.5036939
Produced by FastQC (version 0.11.2)