FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_female_transmission_spinal_cord_pcr3.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_female_transmission_spinal_cord_pcr3.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences493966
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

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GTATAGATAAGGGAAGCTCCTGCCAGATAGCTTCCTCTGAAGATGTTGCA38880.7870987071984711No Hit
TATCTATACAGTGACGAGAAACGCTGGCCTGGTTAAGAGACGTGGAGGTG25370.5135981018936526No Hit
ACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCCAG18020.3648024357951762No Hit
CCATAAGTCCTCCCTTTTTCCTAGATAGGGAATGTCTGTCCATTTTGTTA17800.36034868796637826No Hit
GTATAAAGGTGCTGTGCCCATACACCAGCACTATGATGGAAACCATGGAG16720.33848483498864296No Hit
CCTTTATACAGAAGGCCCCTGGTCTTTTTTCAAGCCAGTCCCCCACCATA13920.28180077171303286No Hit
GATAAGGGAAGCTCCTGCCAGATAGCTTCCTCTGAAGATGTTGCACAGTG12980.2627711218990781No Hit
ATACAGGACATGGGCCTACCATGGGAGCTACGAAGCCCCCACGCAAGGAT12230.24758789066453968No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG11460.23199977326374688No Hit
ACCATGGGATTCTCAATGGACATTGATCTGCGGCCAGCCTCCGCCTGGGC10700.21661409894608133No Hit
CTGTATAGATAAGGGAAGCTCCTGCCAGATAGCTTCCTCTGAAGATGTTG10670.2160067696966998No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT10580.21418478194855517No Hit
ATTCCACACCATGAGCATGTCCTCAGTGGTCATCCATTCTCCCTTTCCAT10380.2101359202860116No Hit
GTCCTGTATGGGTGGTTTTCATCAAGAAACCATGTTTCTGCATGTTCATT10270.20790904637161262No Hit
TCTCTACACACTTCAGTGATACCTGACTTTTTATAAGAGTAGAACTCCAG10080.20406262779219622No Hit
TCACTGAAGTGTGTAGAGAGGAGGCTCGCCGTGCCCTCAAGGATGGAGTG9170.18564030722762295No Hit
GGTGTGGACCCTTCCTCACCCAAGTAGCGGACTTGGGTGGATAGATAGTC9140.18503297797824142No Hit
ATCTAATGGGAAGGAGAGAAGAAGGAGCAACCATGGGATTCTCAATGGAC9020.1826036609807153No Hit
CCATGTTGACTGTGTCTTTGATGTTTTCAGCCCAAGTGGTGCGGGGTCTG9010.1824012178975881No Hit
AGTCCGCTACTTGGGTGGATAGATAGTCCATGTACTTTTCTTCATCACCT8970.1815914455650794No Hit
GTTGTACACACAGCTGTGACACTCTCCTCTCAGGTGGTGTTCTCTCTCCC8730.17673281157002707No Hit
GTGTAGAGAGGAGGCTCGCCGTGCCCTCAAGGATGGAGTGGCCACAGGAG8320.16843264516181275No Hit
CTTCAGTGATACCTGACTTTTTATAAGAGTAGAACTCCAGGGCCGACATC8180.16559844199803225No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA8180.16559844199803225No Hit
CTACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCC8090.16377645424988765No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG7950.16094225108610716No Hit
CTCTATTCCACACCATGAGCATGTCCTCAGTGGTCATCCATTCTCCCTTT7790.1577031617560723No Hit
TCCCTTATCTATACAGTGACGAGAAACGCTGGCCTGGTTAAGAGACGTGG7690.15567873092480047No Hit
TCTATACAGTGACGAGAAACGCTGGCCTGGTTAAGAGACGTGGAGGTGGG7680.1554762878416733No Hit
TACCAAAACAAAGTGGTGAAGGTTCTCAGACCAGCTGAAGGAGGAAAAAC7440.150617653846621No Hit
CTCCAGTGCTGTGCTGCTGCGGACCGCCTGGGGATGGGGGGAGGCTGGAG7420.15021276768036668No Hit
GTACCAGATGGCGCGGCTACCTTTTGCTTTCCCGAACTCTCCTTGCTTCT7310.1479858937659677No Hit
ATTTTATGCATGGGACCTTGGAGTCCCGCTGCTAATGATGGGTTGCTATT7230.14636634910095025No Hit
GTAATGAACATAGTCTCTTCCTGGCTGTGGAAGGAGCTGGGGAAACGCAA6940.1404954996902621No Hit
GAATAGTGGTAACTGACATTGACACAATGACAATAGACCCCCAGGTGGAG6880.139280841191499No Hit
CCTATGATCCTGCGCACCATGTTGACTGTGTCTTTGATGTTTTCAGCCCA6880.139280841191499No Hit
GTGTACAACATGATGGGAAAAAGAGAAAAGAAGCAAGGAGAGTTCGGGAA6830.13826862577586313No Hit
ATCTGGTACATGTGGTTGGGAGCCAGATTCTTGGAGTTTGAAGCCCTTGG6820.13806618269273593No Hit
CCCGAACTCTCCTTGCTTCTTTTCTCTTTTTCCCATCATGTTGTACACAC6800.13766129652648157No Hit
GTATTTAATCACGGCCAACGCCAGAGTTCTGTGCCCTTCCTCCATTTGGT6790.1374588534433544No Hit
TCCCAGGAGGAGCTGACTTGTGGTGGACACACTTTTTATGATGTTGCTCT6770.13705396727710004No Hit
ATCCACTAGGGCCCAAAACCTTGGATCATTCACAGCTTCCACAGCCGTCT6770.13705396727710004No Hit
GGGAAGGAGAGAAGAAGGAGCAACCATGGGATTCTCAATGGACATTGATC6650.1346246502795739No Hit
GACTAATCCTCCCCCATGCCTACGTTGCAGTCGCTCCATGGTTTCCATCA6630.13421976411331954No Hit
GAGTTCGGGAAAGCAAAAGGTAGCCGCGCCATCTGGTACATGTGGTTGGG6580.13320754869768364No Hit
TCCCCAGGCGGTCCGCAGCAGCACAGCACTGGAGATGGCTACTGCTATGA6550.1326002194483021No Hit
CTCTATGGTGGGGGACTGGCTTGAAAAAAGACCAGGGGCCTTCTGTATAA6540.13239777636517494No Hit
TTCCTCACCCAAGTAGCGGACTTGGGTGGATAGATAGTCCATGTACTTTT6540.13239777636517494No Hit
CTATAAGGGATCCACACCATAAGTCCTCCCTTTTTCCTAGATAGGGAATG6480.13118311786641185No Hit
CTGTATAAAGGTGCTGTGCCCATACACCAGCACTATGATGGAAACCATGG6410.1297660162845216No Hit
ATTAAATACACATACCAAAACAAAGTGGTGAAGGTTCTCAGACCAGCTGA6360.12875380086888571No Hit
ACCATAGAGAGCACTCTGAGTGTTCGTGTCTCTTCCACTTCAGGACTAGA6340.12834891470263135No Hit
GGTTAAGAGACGTGGAGGTGGGACGGGAGAGACTCTGGGAGAGAAGTGGA6050.12247806529194316No Hit
TGGTAGGCCCATGTCCTGTATGGGTGGTTTTCATCAAGAAACCATGTTTC6050.12247806529194316No Hit
GCCCAAGTGGTGCGGGGTCTGTGCCCTATAAGGGATCCACACCATAAGTC6040.12227562220881599No Hit
TTTATACAGAAGGCCCCTGGTCTTTTTTCAAGCCAGTCCCCCACCATAGA6040.12227562220881599No Hit
GTGTTACTCATAGCAGTAGCCATCTCCAGTGCTGTGCTGCTGCGGACCGC6030.12207317912568882No Hit
CCACTATTCCATCCACAACGGGATTCTTCATGATGCCAGCTGCTGTCCTT5990.1212634067931801No Hit
CTATGGTGGGGGACTGGCTTGAAAAAAGACCAGGGGCCTTCTGTATAAAG5950.12045363446067138No Hit
GTTCATTACCTGGCGAGTGCCTTCTTGGGGATCTGGCACCCTGGTGTCCA5930.12004874829441702No Hit
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC5890.1192389759619083No Hit
CATCTAATGGGAAGGAGAGAAGAAGGAGCAACCATGGGATTCTCAATGGA5870.11883408979565396No Hit
CACAAAGGGAGGTCCCGGTCATGAAGAACCCATGCTGGTGCAAAGCTATG5780.11701210204750935No Hit
TCTAATGGGAAGGAGAGAAGAAGGAGCAACCATGGGATTCTCAATGGACA5710.1155950004656191No Hit
GGATTAGTCAGAGTGCCATTGTCTCGCAACTCCACACATGAGATGTACTG5670.11478522813311037No Hit
GTACACACAGCTGTGACACTCTCCTCTCAGGTGGTGTTCTCTCTCCCTAT5660.11458278504998319No Hit
CTCTTAACCAGGCCAGCGTTTCTCGTCACTGTATAGATAAGGGAAGCTCC5640.11417789888372885No Hit
GAGTAGAACTCCAGGGCCGACATCTGATTCAGACGAGCTTTCCACTTCTC5620.11377301271747449No Hit
TTCTAGAAGAAATGAATCGGGCACCAGGAGGAAAGATGTACGCAGATGAC5590.11316568346809294No Hit
GGAGAGAAGAAGGAGCAACCATGGGATTCTCAATGGACATTGATCTGCGG5580.11296324038496577No Hit
GTACTGGGTCTCTGGGGCAAAGAGCAACATCATAAAAAGTGTGTCCACCA5570.11276079730183858No Hit
GTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGGG5540.11215346805245704No Hit
GAAGAGACCTTCGACTGATGGCTAATGCCATTTGCTCGGCTGTGCCAGTT5500.11134369571994833No Hit
TCATACAACAACTACTCCTTAATGGCGATGGCCACACAAGCTGGAGTGCT5440.11012903722118526No Hit
CTCTAACACTTCCTCAGCTTCCATGTTCCGGATAAGCTGCACCACCAAGT5380.10891437872242218No Hit
CCATAGAGAGCACTCTGAGTGTTCGTGTCTCTTCCACTTCAGGACTAGAT5370.10871193563929502No Hit
ACACCACACCATACGGCCAACAAAGAGTCTTCAAAGAAAAAGTGGACACC5240.10608017555864169No Hit
GACTGACACCACACCATACGGCCAACAAAGAGTCTTCAAAGAAAAAGTGG5230.10587773247551452No Hit
CTATTCCACACCATGAGCATGTCCTCAGTGGTCATCCATTCTCCCTTTCC5230.10587773247551452No Hit
TTTTATAAGAGTAGAACTCCAGGGCCGACATCTGATTCAGACGAGCTTTC5230.10587773247551452No Hit
CTTTTTATGATGTTGCTCTTTGCCCCAGAGACCCAGTACATCTCATGTGT5170.10466307397675144No Hit
TCACTGTATAGATAAGGGAAGCTCCTGCCAGATAGCTTCCTCTGAAGATG5140.1040557447273699No Hit
TCTCTTAACCAGGCCAGCGTTTCTCGTCACTGTATAGATAAGGGAAGCTC5140.1040557447273699No Hit
CGTTGTACACACAGCTGTGACACTCTCCTCTCAGGTGGTGTTCTCTCTCC5140.1040557447273699No Hit
TCCCAAGGCTTTGACAGGAGTCTAACAACCCCGTTCACGAGGGAAGACGC5130.10385330164424272No Hit
GTTAGACTCCTGTCAAAGCCTTGGGACGTGGTGACTGGAGTTACAGGAAT5100.10324597239486119No Hit
GTCCTGAAGTGGAAGAGACACGAACACTCAGAGTGCTCTCTATGGTGGGG5100.10324597239486119No Hit
TTCCTAGATAGGGAATGTCTGTCCATTTTGTTACAGGAGTCTTGTCCTCC5070.10263864314547964No Hit
CCATGAGCATGTCCTCAGTGGTCATCCATTCTCCCTTTCCATGGATTGAC5060.10243620006235246No Hit
TTTCAAGACAAGACCAGAGAGGGAGTGGACAAGTTGTCACTTATGCTCTC5040.10203131389609811No Hit
GGATAGACTCAAACGAATGGCGGTCAGTGGAGATGACTGCGTTGTGAAGC5030.10182887081297094No Hit
CTTCAAATATTGCTCCCAGTGCTGCATTGCTGCGCACCTTGTTGATAAAC4990.10101909848046221No Hit
ACCATGGGAGCTACGAAGCCCCCACGCAAGGATCAGCGTCTTCCCTCGTG4990.10101909848046221No Hit
TAAATACACATACCAAAACAAAGTGGTGAAGGTTCTCAGACCAGCTGAAG4970.10061421231420786No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT4940.10000688306482633No Hit
GTGTTAGAGATGCAAGACTTATGGTTGTTGAGGAAGCCAGAGAAAGTGAC4940.10000688306482633No Hit

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CATCTAA450.0128.013411
ATCTAAT1650.096.0100561
TCCGGGT259.6453284E-486.40032
GGACCCT2250.080.0002756
TGTGGAC2350.079.659863
TGGACCC2300.078.261155
GTGGACC2300.078.261154
GACCCTT2300.078.253237
TCTAATG2300.068.869812
CCGGGTG350.003664479161.7145083
TAATGGG2600.060.923294
CTAATGG2600.060.923293
AGTCCGC2600.058.159941
TACTTGG2600.058.1481678
CGCTACT2750.054.982015
CTCCGGG400.00621439154.0056571
TCCGCTA2850.053.052823
CCGCTAC2850.053.052824
CTACTTG2850.053.0474477
GTCCGCT2900.052.1381152
Produced by FastQC (version 0.11.2)