FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n02_male_transmission_spinal_cord_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n02_male_transmission_spinal_cord_pcr2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences276300
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
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC36611.325009048136084No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC8060.2917119073470865No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA7050.255157437567861No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA6600.23887079261672098No Hit
TCATCAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTG6210.22475570032573292No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC6190.22403184943901558No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG5680.20557365182772347No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC5640.2041259500542888No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGAGAGAGTCATCT5550.20086862106406084No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA5410.19580166485703943No Hit
CATCAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC5370.19435396308360475No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA5350.19363011219688744No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC5030.18204849800941006No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA4940.17879116901918204No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT4940.17879116901918204No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC4790.17336228736880205No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC4760.17227651103872604No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC4690.16974303293521534No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG4690.16974303293521534No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC4560.16503800217155265No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGACTGTTTCCAGTGACTTCCGC4560.16503800217155265No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC4540.16431415128483534No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT4530.16395222584147667No Hit
CCATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTG4500.16286644951140067No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT4390.1588852696344553No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC4310.15598986608758594No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC4280.15490408975750997No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT4270.1545421643141513No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG4250.15381831342743396No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA4110.14875135722041258No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG4070.1473036554469779No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC3940.14259862468331524No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT3830.13861744480636987No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA3770.13644589214621788No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG3720.13463626492942454No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC3670.1328266377126312No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA3640.1317408613825552No Hit
GCCTTATAAGGCCTGCTTCCAGTCTCTGCTCGCATGAGCACGGCGAGGTT3610.1306550850524792No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG3610.1306550850524792No Hit
GCACGCGCTGCTGCCGCTTGTAGGCCTGGGATCAAGTACATGTAGTGCGC3550.12848353239232718No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG3490.12631197973217517No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG3480.1259500542888165No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC3460.12522620340209917No Hit
TCTTCTGTCTGTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCC3430.12414042707202316No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC3400.12305465074194716No Hit
GGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCT3390.12269272529858849No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG3380.12233079985522982No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG3380.12233079985522982No Hit
GTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCCAGACGGGAAG3350.12124502352515382No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG3340.12088309808179515No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG3300.11943539630836049No Hit
CATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTGC3250.11762576909156715No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA3130.11328266377126311No Hit
ATGTTAGTGCTATAACCCAGGGAAAGAGGGAGGAGGAGACTCCGGTTGAA3120.11292073832790445No Hit
GTTGTAGTAAGCGTGAAGTGAAAGTGGCATGGCACATCAAATCAACGATT3020.10930148389431778No Hit
GCCTTGAAGTTGGCGCCCATCTCTGAGATGTCAGTTGTTATGACAAAGTC3010.10893955845095911No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT3000.10857763300760044No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC2990.10821570756424177No Hit
GAGTATGATCTCTCTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAAT2960.10712993123416577No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC2930.10604415490408976No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC2930.10604415490408976No Hit
ATACTTGAGGGGTCTGTGAAGTGGGCTTCATCCATGATGTAGAGATTGTA2900.10495837857401374No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC2900.10495837857401374No Hit
GTATGGATCAAGTCTTCCCTCACCGCTCCTCAGTGCGGCTCCTTTTGTAA2900.10495837857401374No Hit
GATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGA2890.10459645313065508No Hit
GGGTTATAGCACTAACATAGCTTCCATTCTTGATCACAACCCCATTGCCA2870.10387260224393774No Hit
ATCATGGACACAGAAGTGGAAGTCCCAGAGAGAGCCTGGAGCTCAGGCTT2860.10351067680057907No Hit
CTCCATACTTTGTCCACACCTCTGCTGGTACGCTGTCTTCCATTATGGTG2820.1020629750271444No Hit
ATTTCAGGAAGAACTCTCCTGGTTTTTCCGGCTCCTGGATGCAGATCCAA2810.10170104958378573No Hit
GCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGG2790.10097719869706841No Hit

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCTTTTG100.007237697143.990591
AGATAAG1100.0104.720431
TCATCAA950.083.362971
CTTTGTA300.001988605671.995292
ACTGGAG8300.056.3818553
CCCAGGA2050.056.1812829
TGGAGAT9000.052.796555
CTGGAGA8900.052.5808334
TTGATGA657.5838267E-444.30484
GATGAGG657.5838267E-444.30486
TCTGAAC3950.034.6306463
CTGAACA3950.034.6306464
TGAACAG4000.034.1977655
GAACAGA3800.034.103036
AACAGAC3800.034.103037
TACAACC3900.033.2285964
TAATGAG3550.032.4485865
CTACAAC4000.032.397883
GGAGATG18650.031.2687366
TACTACA4150.031.2268751
Produced by FastQC (version 0.11.2)