FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_male_transmission_spinal_cord_pcr1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_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
GAATGGTTTTGGCGATACTAGCCTTTTTGAGATTTACAGCAATCAAGCCA24300.4124397252438571No Hit
ATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGCAACAC16860.2861618834407996No Hit
GTATTACCTGACCATGAACAATAAGCATTGGTTGGTGCACAAAGAGTGGT15580.26443666334564997No Hit
GGTAATACAGATCTGAAAAGTCAAGGCCTGTCCTTGGTTCACAGTCAAGT15300.25968427144983597No Hit
CTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTA14590.2476335634283076No Hit
GTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCAGGCAATGGCAA14130.2398260624566132No Hit
TCCGTACACAACCCAAGTTGATGTCGTGTTGCACCAGCAATCGACATCAT13350.22658725646113137No Hit
CTTTATTGTTCCAGTGTGGAGTTCCGGTGTCTGCCCCAGCATGCCAAGGC13210.22421106051322437No Hit
CCATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTG12370.2099538848257824No Hit
TCTCACAGTGGCCTCAAATGCCTTTCCGATGGTGCTACCACTCCTATGCC11430.1939994263184069No Hit
ATCTAAGCTTGTCCATTTTTAGGCGGCATTTCAAGTGGCCAGAGAACAGC11260.1911140455245198No Hit
GAGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCG11230.19060486067853974No Hit
TCCTTGTAGAGTGAGAAGGGAGCGTCACGGCTCTTCTAGATCGCCGTGCC11220.19043513239654636No Hit
AGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGGATTTG10970.18619192534671244No Hit
GTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGCATAGGAGTGG10870.18449464252677888No Hit
GTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAAATCC10480.17787523952903797No Hit
GAATATGACACGCCCTTCAATCTAAGCTTGTCCATTTTTAGGCGGCATTT10450.17736605468305788No Hit
ACTCTATGTCAACTGTTGGCTTGTCCTGTGCCATCACGGTAACGCAGCCT10250.17397148904319076No Hit
TCTTAGAACACGTAAACTTGGCACATGTCACCAAGCTCCCTTTGCCAAAA10130.17193474965927047No Hit
TTCATATCCTGTATCATTGACAATCATCCCGCTATGCTGGGAGCCATGCA10050.17057692340332362No Hit
GTCATGGACCCATCAGAATGGTTTTGGCGATACTAGCCTTTTTGAGATTT9750.1654850749435229No Hit
ACAACAAAGAGGCATTGGTAGAATTCAAGGATGCCCACGCCAAGAGGCAA9640.163618063841596No Hit
TCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAAA9600.16293915071362255No Hit
GTACAGATCATGGACCTCGGGCACATGTGTGACGCCACCATGAGTTATGA9450.1603932264837222No Hit
ACACAAGGTGAGGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTG9160.15547110630591487No Hit
CTACAAGGAAGTTGCAAACGCGGTCGCAGACCTGGTTAGAATCAAGAGAA9130.1549619214599348No Hit
TCCCTTAACAGCTGTTCCTATGACGGCTGGGTCACATTCTAATGAGTAAT9070.15394355176797464No Hit
GTTAGTAACATGGCCGAGGTAAGATCCTATTGCTACGAGGCATCGATATC8990.15258572551202781No Hit
GTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTGTAGTCA8870.15054898612810752No Hit
CTCAATATGTCTGCAAAAGAACATTAGTGGACAGAGGTTGGGGAAACGGT8860.15037925784611414No Hit
CCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGA8830.14987007300013408No Hit
ATCTAGAAGAGCCGTGACGCTCCCTTCTCACTCTACAAGGAAGTTGCAAA8740.14834251846219387No Hit
CATTAATGAGGACCATCAAGTCACCTTCAAGAGCAGAGATCGCAGTTTGC8570.14545713766830679No Hit
TTCCAAGACAACATCAACCCAGGTCCCACCTGACATGCCCTCCACGAAGT8520.14460849625834002No Hit
GGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATTGGGAG8510.14443876797634667No Hit
CATATTGAGTGTCTGATTGCTTGTCAAGGTAGGCCTCACCTTGTGTTGGG8360.1418928437464463No Hit
GCATACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTT8310.14104420233647955No Hit
GTACAAGTACCATCCTGACTCCCCCCGCAGATTGGCAGCAGCAGTCAAGC8270.1403652892085061No Hit
GGCCTGGGAAGAGGGGATCTGTGGGATCTCATCCGTTTCAAGAATGGAAA8190.13900746295255925No Hit
GTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAGAGGGTTACAGAA8120.13781936497860575No Hit
CTTCTAGATCGCCGTGCCTCACCTTTTTTGTGATGACAGGTTCCGTACAC8100.13747990841461905No Hit
AGCTTAGATTGAAGGGCGTGTCATATTCCTTGTGCACTGCGGCATTCACA8100.13747990841461905No Hit
CTCCAAGAGAGAAGTGGTCCATATGATCGGTTGACCCCGCTGTCACCATT8090.13731018013262566No Hit
TTCTTACATTGTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGC8080.13714045185063234No Hit
TACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGC8070.13697072356863896No Hit
CTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTTTTG8070.13697072356863896No Hit
ATCCAGCATAGGGCACTCATAACTCATGGTGGCGTCACACATGTGCCCGA8040.1364615387226589No Hit
TCCATGCTCTGTGCTCAAGCGGACATTCCTTCAGTGTGTCACCGTCGACA7850.1332367013647851No Hit
ATCATGACCAAGTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCA7760.1317091468268449No Hit
ATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTT7740.1313696902628582No Hit
GTTCGAGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGG7720.13103023369887146No Hit
ATATCGGACATGGCTTCGGACAGTCGTTGCCCAACACAAGGTGAGGCCTA7670.1301815922889047No Hit
ACCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATG7460.12661729836704422No Hit
TAATAAAGAAGTTCAAGAAAGATCTTGCTGCCATGTTGAGAATAATCAAT7460.12661729836704422No Hit
GTATCAGGTGCATTGGAGTCAGCAATAGAGACTTCGTGGAGGGCATGTCA7430.12610811352106413No Hit
GTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGTATCAG7400.12559892867508407No Hit
GTGTACGGAACCTGTCATCACAAAAAAGGTGAGGCACGGCGATCTAGAAG7340.12458055898312392No Hit
ATCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAA7320.12424110241913722No Hit
GTTACTAACCGTCGTCGTGACCAACTCTATGTCAACTGTTGGCTTGTCCT7310.12407137413714385No Hit
TTCCTTCAGTGTGTCACCGTCGACAACAAAACTGTTGTTGGTCTTTGCCG7250.1230530044451837No Hit
GCTAAAGACTTGGGTATGATAAGATCACTTTCTTCTACTCCATCTGTCCA7250.1230530044451837No Hit
AGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGA7210.12237409131721026No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG7090.12033735193329No Hit
TCCCAGGCCTGCTTGACTGCTGCTGCCAATCTGCGGGGGGAGTCAGGATG7090.12033735193329No Hit
GTCATATTCCTTGTGCACTGCGGCATTCACATTCACCAAGGTCCCAGCTG7060.11982816708730994No Hit
GGATATGAAACTGACGAAAATAGAGCGAAAGTCGAGGTTACGCCTAATTC7050.11965843880531657No Hit
GTCAGTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAA7020.1191492539593365No Hit
TACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATT6950.11796115598538301No Hit
GATCTGTACGTGGCACTTGTTCACTCCCAATGTGGTAGCAAACGAAATGG6900.1171125145754162No Hit
TTAGTGGACAGAGGTTGGGGAAACGGTTGTGGACTTTTTGGCAAAGGGAG6880.1167730580114295No Hit
GTTCTAAGAAGATGACCGGGAAGAGCATTCAACCGGAAAATCTGGAGTAT6800.11541523175548266No Hit
GTATCAACAGGTTTAATTTGGATTTGGAAACGAGAGTTTCTGGTCATGAA6800.11541523175548266No Hit
CTCATAACTCATGGTGGCGTCACACATGTGCCCGAGGTCCATGATCTGTA6790.11524550347348929No Hit
GTTAAGGGAAGGGAGGCCGCGCACAGTGATCTGGGCTATTGGATTGAAAG6730.11422713378152914No Hit
GCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGC6730.11422713378152914No Hit
CTCACGGGGTGTCCAATTGGCTCTGAAAATGAAGGAGACCAGCAAGGCTG6610.11219039439760888No Hit
CACTAGCAGCGTGCCTATGAGGATCTGTGAGAACCAGGACATTCCTCCAA6600.11202066611561551No Hit
GGGTAAGGGCATTCACCAGATTTTTGGAGCAGCCTTCAAATCACTGTTTG6460.10964447016770852No Hit
CTTCCACACCAGTGTCTGGCTTAAGGTCAGAGAAGATTACTCATTAGAAT6380.10828664391176167No Hit
GGTGTGGAAGACTCCAAACCCGTGATCCTCCACAAGAAAACTATTCCATG6370.1081169156297683No Hit
TATCAACAGATGGGGTTCCGTGGGGAAAAAAGAGGCTATGGAAATAATAA6320.10726827421980152No Hit
GTTGAGAATAATCAATGCTAGGAAAGAGAGGAAGAGACGTGGCGCAGACA6280.10658936109182808No Hit
GTCCACAATGTGTGAGACTTTGGCCATTCACATGTTTTCATCTCAATCAG6250.106080176245848No Hit
GTACATGTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTG6250.106080176245848No Hit
TATCATACCCAAGTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAG6190.10506180655388787No Hit
GACTACAGCCATGGCAGCAGAGATCACTAGACGCGGGAGTGCATACTACA6130.10404343686192775No Hit
CTCCTATGCCAGTGGTGGGTGATTTTCTTGTCCCCAACTCCTATGACAAT6090.10336452373395431No Hit
CATTGGGAGTGAACAAGTGCCACGTACAGATCATGGACCTCGGGCACATG6070.10302506716996761No Hit
GTCCTGTGCCATCACGGTAACGCAGCCTCCATGTTCCAAGACAACATCAA6050.10268561060598087No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC5990.10166724091402075No Hit
ATGCAGGGACAGATGGACCCTGCAAGATCCCAGTCCAGATGGCGGTGGAC5960.10115805606804068No Hit
CCCTACAGCACCATTCCTCAATGACCCTTCCACTTGCAGTAGTTGATCTC5960.10115805606804068No Hit
CTCCTGCACCATGAGTAGAATCACAAGCACTCCAAGAGAGAAGTGGTCCA5940.10081859950405395No Hit
GCATACTGCACCTCCACTGTGACTGTTCCATGCAGTGTTTCAGCTGGGAC5930.1006488712220606No Hit

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GGGTAGG100.0072357077144.017581
TTTATTG1850.089.509252
GCGACAG259.6417166E-486.4105451
GTCAGTG1250.086.4105451
CAGTGCG1250.086.3958743
AGTGCGT1300.083.072964
TGCGTGG3350.075.220292
GTTCGAG1550.074.331651
CGACAGT608.413008E-872.008791
TCGAGTC1700.071.996563
GTGCGTG3550.070.9945761
CGAGTCT1750.069.9395144
TTCGAGT1700.067.761472
GCGTGGC3750.067.1967853
ACAGTTC651.4660873E-766.458373
AGTCTGA3250.059.822681
GTCTGAA3300.058.906282
GAGTCTG2100.058.282935
AGTTCGA753.9439146E-757.597255
TCTGAAG3500.055.5402073
Produced by FastQC (version 0.11.2)