FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n02_male_transmission_spinal_cord_pcr1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n02_male_transmission_spinal_cord_pcr1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences589177
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
GAATGGTTTTGGCGATACTAGCCTTTTTGAGATTTACAGCAATCAAGCCA24130.40955434444997No Hit
ATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGCAACAC16160.2742809037012647No Hit
GTATTACCTGACCATGAACAATAAGCATTGGTTGGTGCACAAAGAGTGGT16140.2739414471372779No Hit
GGTAATACAGATCTGAAAAGTCAAGGCCTGTCCTTGGTTCACAGTCAAGT14550.2469546503003342No Hit
CTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTA13690.23235801804890552No Hit
GTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCAGGCAATGGCAA12150.20621986262192854No Hit
GAGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCG11890.2018069272901013No Hit
TCCGTACACAACCCAAGTTGATGTCGTGTTGCACCAGCAATCGACATCAT11240.19077458896053306No Hit
AGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGGATTTG10820.1836460011168121No Hit
ATCTAAGCTTGTCCATTTTTAGGCGGCATTTCAAGTGGCCAGAGAACAGC10770.18279735970684532No Hit
CCATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTG10570.17940279406697818No Hit
TTCATATCCTGTATCATTGACAATCATCCCGCTATGCTGGGAGCCATGCA10220.17346230419721068No Hit
TCCTTGTAGAGTGAGAAGGGAGCGTCACGGCTCTTCTAGATCGCCGTGCC10200.17312284763322397No Hit
CTTTATTGTTCCAGTGTGGAGTTCCGGTGTCTGCCCCAGCATGCCAAGGC10050.17057692340332362No Hit
GTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGCATAGGAGTGG10000.16972828199335682No Hit
GTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAAATCC9960.1690493688653834No Hit
TCTCACAGTGGCCTCAAATGCCTTTCCGATGGTGCTACCACTCCTATGCC9950.16887964058339006No Hit
ACTCTATGTCAACTGTTGGCTTGTCCTGTGCCATCACGGTAACGCAGCCT9860.16735208604544985No Hit
TCTTAGAACACGTAAACTTGGCACATGTCACCAAGCTCCCTTTGCCAAAA9500.161241867893689No Hit
GTACAGATCATGGACCTCGGGCACATGTGTGACGCCACCATGAGTTATGA9410.1597143133557488No Hit
GTTAGTAACATGGCCGAGGTAAGATCCTATTGCTACGAGGCATCGATATC9090.15428300833196135No Hit
GTCATGGACCCATCAGAATGGTTTTGGCGATACTAGCCTTTTTGAGATTT9050.15360409520398793No Hit
GTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTGTAGTCA8630.14647550736026693No Hit
CCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGA8570.14545713766830679No Hit
GAATATGACACGCCCTTCAATCTAAGCTTGTCCATTTTTAGGCGGCATTT8550.14511768110432008No Hit
GTACAAGTACCATCCTGACTCCCCCCGCAGATTGGCAGCAGCAGTCAAGC8480.1439295831303666No Hit
TCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAAA8340.1415533871824596No Hit
TCCCTTAACAGCTGTTCCTATGACGGCTGGGTCACATTCTAATGAGTAAT8330.14138365890046625No Hit
ATCATGACCAAGTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCA8320.14121393061847287No Hit
CTCAATATGTCTGCAAAAGAACATTAGTGGACAGAGGTTGGGGAAACGGT8300.14087447405448617No Hit
ACAACAAAGAGGCATTGGTAGAATTCAAGGATGCCCACGCCAAGAGGCAA8200.1391771912345526No Hit
CTTCTAGATCGCCGTGCCTCACCTTTTTTGTGATGACAGGTTCCGTACAC8100.13747990841461905No Hit
ATCCAGCATAGGGCACTCATAACTCATGGTGGCGTCACACATGTGCCCGA8080.13714045185063234No Hit
TACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGC8010.1359523538766788No Hit
GCATACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTT7940.13476425590272534No Hit
ATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTT7840.13306697308279175No Hit
GGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATTGGGAG7700.13069077713488475No Hit
ACACAAGGTGAGGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTG7670.1301815922889047No Hit
CTACAAGGAAGTTGCAAACGCGGTCGCAGACCTGGTTAGAATCAAGAGAA7660.13001186400691134No Hit
GGCCTGGGAAGAGGGGATCTGTGGGATCTCATCCGTTTCAAGAATGGAAA7610.12916322259694454No Hit
CTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTTTTG7600.1289934943149512No Hit
TTCCAAGACAACATCAACCCAGGTCCCACCTGACATGCCCTCCACGAAGT7570.12848430946897113No Hit
ATCTAGAAGAGCCGTGACGCTCCCTTCTCACTCTACAAGGAAGTTGCAAA7510.12746593977701098No Hit
CATATTGAGTGTCTGATTGCTTGTCAAGGTAGGCCTCACCTTGTGTTGGG7470.12678702664903754No Hit
GTTCGAGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGG7400.12559892867508407No Hit
AGCTTAGATTGAAGGGCGTGTCATATTCCTTGTGCACTGCGGCATTCACA7390.1254292003930907No Hit
CTCCAAGAGAGAAGTGGTCCATATGATCGGTTGACCCCGCTGTCACCATT7330.12441083070113056No Hit
GTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGTATCAG7190.12203463475322356No Hit
ATCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAA7180.12186490647123022No Hit
CATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTGC7140.12118599334325678No Hit
GTTACTAACCGTCGTCGTGACCAACTCTATGTCAACTGTTGGCTTGTCCT7130.12101626506126342No Hit
GTTGAGAATAATCAATGCTAGGAAAGAGAGGAAGAGACGTGGCGCAGACA7100.12050708021528335No Hit
GGATATGAAACTGACGAAAATAGAGCGAAAGTCGAGGTTACGCCTAATTC7060.11982816708730994No Hit
GATCTGTACGTGGCACTTGTTCACTCCCAATGTGGTAGCAAACGAAATGG7050.11965843880531657No Hit
TTCTTACATTGTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGC6880.1167730580114295No Hit
TCCATGCTCTGTGCTCAAGCGGACATTCCTTCAGTGTGTCACCGTCGACA6860.11643360144744279No Hit
GTATCAGGTGCATTGGAGTCAGCAATAGAGACTTCGTGGAGGGCATGTCA6850.11626387316544942No Hit
GCTAAAGACTTGGGTATGATAAGATCACTTTCTTCTACTCCATCTGTCCA6720.1140574054995358No Hit
CTCCTATGCCAGTGGTGGGTGATTTTCTTGTCCCCAACTCCTATGACAAT6670.11320876408956902No Hit
GTCATATTCCTTGTGCACTGCGGCATTCACATTCACCAAGGTCCCAGCTG6670.11320876408956902No Hit
GTGTACGGAACCTGTCATCACAAAAAAGGTGAGGCACGGCGATCTAGAAG6650.11286930752558229No Hit
GTTCTAAGAAGATGACCGGGAAGAGCATTCAACCGGAAAATCTGGAGTAT6640.11269957924358895No Hit
TACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATT6640.11269957924358895No Hit
AGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGA6630.11252985096159558No Hit
CACTAGCAGCGTGCCTATGAGGATCTGTGAGAACCAGGACATTCCTCCAA6570.11151148126963543No Hit
ACCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATG6550.11117202470564873No Hit
GTCAGTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAA6540.11100229642365536No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG6470.10981419844970187No Hit
ATATCGGACATGGCTTCGGACAGTCGTTGCCCAACACAAGGTGAGGCCTA6450.10947474188571515No Hit
CTCATAACTCATGGTGGCGTCACACATGTGCCCGAGGTCCATGATCTGTA6440.10930501360372182No Hit
GCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGC6440.10930501360372182No Hit
GTATCAACAGGTTTAATTTGGATTTGGAAACGAGAGTTTCTGGTCATGAA6390.10845637219375501No Hit
TTAGTGGACAGAGGTTGGGGAAACGGTTGTGGACTTTTTGGCAAAGGGAG6370.1081169156297683No Hit
GTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAGAGGGTTACAGAA6200.10523153483588124No Hit
TAATAAAGAAGTTCAAGAAAGATCTTGCTGCCATGTTGAGAATAATCAAT6170.10472234998990117No Hit
GTACATGTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTG6120.10387370857993439No Hit
GGGTAAGGGCATTCACCAGATTTTTGGAGCAGCCTTCAAATCACTGTTTG6110.10370398029794102No Hit
TTCCTTCAGTGTGTCACCGTCGACAACAAAACTGTTGTTGGTCTTTGCCG6000.1018369691960141No Hit
TATCAACAGATGGGGTTCCGTGGGGAAAAAAGAGGCTATGGAAATAATAA5940.10081859950405395No Hit
GACTACAGCCATGGCAGCAGAGATCACTAGACGCGGGAGTGCATACTACA5900.10013968637608053No Hit

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GTTCGAG1400.087.44251
TCGAGTC1400.087.41283
CGAGTCT1450.084.398574
GCGACAG451.2828095E-680.012741
ACAGTTC451.2854034E-679.9855654
TTCGAGT1550.078.96692
TTTATTG2300.071.999242
AGTGCGT1300.071.9870154
CAGTGCG1300.071.9870153
CGACAGT554.2300017E-665.453852
AGTCTGA2850.060.6412351
AGTTCGA607.0946226E-659.9891746
GAGTCTG2050.059.696555
GTGCGTG2750.057.6091731
GTCTGAA3000.057.599392
GTCAGTG1700.055.067591
TCTGAAG3150.054.8472443
TGCGTGG2900.054.6201132
TGAAGCG3300.054.5356145
CTGAAGC3200.053.990264
Produced by FastQC (version 0.11.2)