FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n02_infko_m-red_spinal_cord_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n02_infko_m-red_spinal_cord_pcr2.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences252946
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
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC32431.2820918298767325No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC7540.2980873387995857No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA6230.24629762874289374No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA5530.2186237378729057No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC5370.2122982771026227No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT5340.21111225320819463No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG5090.20122872075462747No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA5060.20004269686019943No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA4950.19569394258062986No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGAGAGAGTCATCT4830.19094984700291762No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA4720.18660109272334807No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC4710.18620575142520537No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC4630.18304302104006387No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC4490.17750824286606628No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT4300.16999675820135524No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG4220.16683402781621373No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC4180.165252662623643No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT4090.16169459094035882No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGACTGTTTCCAGTGACTTCCGC4060.16050856704593075No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC3930.1553691301700758No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT3830.15141571718864896No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC3820.1510203758905063No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC3800.1502296932942209No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC3790.14983435199607822No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA3780.14943901069793553No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC3550.14034616084065374No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG3470.13718343045551223No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG3450.13639274785922686No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC3430.1356020652629415No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG3400.13441604136851343No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG3380.13362535877222806No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG3380.13362535877222806No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG3360.1328346761759427No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC3350.13243933487780002No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA3260.12888126319451582No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC3240.12809058059823045No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC3160.12492785021308896No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG3150.12453250891494629No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG3110.12295114372237552No Hit
TCTTCTGTCTGTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCC3090.12216046112609015No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT3080.12176511982794747No Hit
GCCTTATAAGGCCTGCTTCCAGTCTCTGCTCGCATGAGCACGGCGAGGTT3080.12176511982794747No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG3040.12018375463537673No Hit
ACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCCAG3020.11939307203909136No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT3020.11939307203909136No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC2970.11741636554837792No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA2970.11741636554837792No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG2910.1150443177595218No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC2890.11425363516323643No Hit
ACCATGGGATTCTCAATGGACATTGATCTGCGGCCAGCCTCCGCCTGGGC2850.11267226997066566No Hit
GCATAAAATGGCATCCCTTTGCCCATGCCAAACAGCACTCCAGCTTGTGT2820.11148624607623761No Hit
ATGTTAGTGCTATAACCCAGGGAAAGAGGGAGGAGGAGACTCCGGTTGAA2810.11109090477809493No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC2740.10832351569109613No Hit
GGTATGAGCACCACCAGTAATAAAAACACAACAATGAGGACACATGCAAT2730.10792817439295344No Hit
GGAGTGTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGG2720.10753283309481074No Hit
GCACGCGCTGCTGCCGCTTGTAGGCCTGGGATCAAGTACATGTAGTGCGC2720.10753283309481074No Hit
GTATGGATCAAGTCTTCCCTCACCGCTCCTCAGTGCGGCTCCTTTTGTAA2680.10595146790224No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC2680.10595146790224No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA2640.10437010270966925No Hit
GGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCT2630.10397476141152658No Hit
ATTTTATGCATGGGACCTTGGAGTCCCGCTGCTAATGATGGGTTGCTATT2610.1031840788152412No Hit
GTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCCAGACGGGAAG2610.1031840788152412No Hit
ATACTTGAGGGGTCTGTGAAGTGGGCTTCATCCATGATGTAGAGATTGTA2600.10278873751709851No Hit
GGGTTATAGCACTAACATAGCTTCCATTCTTGATCACAACCCCATTGCCA2590.10239339621895581No Hit
GCCTTGAAGTTGGCGCCCATCTCTGAGATGTCAGTTGTTATGACAAAGTC2580.10199805492081314No Hit
GCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTGACAGCGG2570.10160271362267045No Hit
TCCTGAAATAGTCCGTGAAGCCATAAAAAAGAGACTCCGGACAGTGATCT2560.10120737232452777No Hit
GCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAACCTGGAGATGA2540.10041668972824239No Hit

[FAIL]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GAGATAA203.972314E-4107.987541
AGATAAG700.0102.845271
ACTGGAG9300.076.606013
TGGAGAT9150.076.288895
CTGGAGA9450.074.628534
TCTGTGC851.3744284E-859.2872772
CTGTGCC902.1645974E-855.9713973
ATTCTAT400.00621630753.993771
AGAAAGA400.006226042353.9724245
GGAGATG17700.044.722916
CCCAGGA1801.8189894E-1243.9775249
CACTGGA17950.041.3099942
GCACTGG19650.038.1024741
ACTACAA3250.037.6571962
TACTACA3250.037.6571961
CTACAAC3250.037.6423033
TACAACC3350.036.5186544
GATGGCT18000.033.582849
GAGATGG22150.031.839267
AGGAAAG1650.030.5298545
Produced by FastQC (version 0.11.2)