FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_infko_m-red_spinal_cord_pcr2.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_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
GCACTGGAGATGGCTACTGCTATGAGTAACACTTGTCCCATCTTCTTCTC35881.4184845777359594No Hit
TACTACAACCCATCAGAGTCCCTAATTACAATCTCTACATCATGGATGAA7400.29255256062558804No Hit
GGTCTGAACAGACCCTAGCATCCATCCATCTCGGTTTGAGCACTCTCTTC6920.2735761783147391No Hit
GTTCAGACCATGCGGCCCTGAAGTCGTTCAAAGAATTCGCCGCTGGAAAA6230.24629762874289374No Hit
TGCTAGTGCTGCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAAC6180.2443209222521803No Hit
CTATTAATGTGGTAGGACTACTGTTACTCACAAGGAGTGGGAAGCGGAGC5840.23087931811532897No Hit
CATTAATAGGGTCTACTACCCTCACAGCTGTCAATCCCAGGGCCATGACA5730.22653056383575942No Hit
TACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCC5620.22218180955618985No Hit
CTCTAGGAGATGCCTAAAACCAGTCATACTTGATGGTGAGAGAGTCATCT5420.21427498359333613No Hit
CTCCTAGAGTCTATGACCCGGTCAGCCTTGAAGTTGGCGCCCATCTCTGA5340.21111225320819463No Hit
CAGTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCT5240.20715884022676775No Hit
GAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGTCATTG5140.2032054272453409No Hit
GGATGAGAGTGGTGATTTCTCCTTGGTAGAGGAAGATGGTCCACCCATGA5110.20201940335091284No Hit
TCTCTGAGATGTCAGTTGTTATGACAAAGTCCCACTCTTGATTTTTTGTT4930.1949032599843445No Hit
AGATAAGGCCCAGGAAAGAACCAGAGAGCAACTTAGTGAGGTCAATGGTG4590.18146165584749316No Hit
ATCTATGCCGCATTGACAACTCTCATCACCCCAGCTGTCCAACATGCGGT4590.18146165584749316No Hit
GTATGACACCAAGTCCTGCTTGACATCCCCCCAGTATGGATCAAGTCTTC4580.18106631454935046No Hit
GCTATGAGTAACACTTGTCCCATCTTCTTCTCCACCTGGGGGTCTATTGT4470.1767175602697809No Hit
CATGTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGC4410.17434551248092478No Hit
GTGTGGAAGACTCCCTCTTGCATGACTCCCACTCCAACCTGTGTTGAACC4340.17157812339392597No Hit
CACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCATGCCAC4270.16881073430692717No Hit
CCCCGTGAGAGCATGCTGCTAGCCCTGGCTTCGTGTCTTCTGCAAACTGC4230.16722936911435643No Hit
TATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTGGA4100.16208993223850152No Hit
ACCCTGCAGGGACCTCAGGATCTCCGATCCTAGACAAATGTGGAAGAGTG4090.16169459094035882No Hit
TCTCAGAGATGGGCGCCAACTTCAAGGCTGACCGGGTCATAGACTCTAGG4070.16090390834407345No Hit
CTCTCATCCAGTGCCACGTCAAGCCGAGGACTGTTTCCAGTGACTTCCGC3950.1561598127663612No Hit
CTTCCACACCATGTGGCACGTTACAAAAGGAGCCGCACTGAGGAGCGGTG3870.1529970823812197No Hit
GATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGATGGCTG3790.14983435199607822No Hit
GTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGCCTGC3760.14864832810165016No Hit
CCTTTTGTAACGTGCCACATGGTGTGGAAGACTCCCTCTTGCATGACTCC3700.14627628031279402No Hit
GCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCCTG3700.14627628031279402No Hit
GTACACTCCATCTGTGGTCTCTCCTTTCTTCACTTCTTTGGGAGCAGGCA3640.1439042325239379No Hit
CTCTACATCATGGATGAAGCCCACTTCACAGACCCCTCAAGTATAGCTGC3620.14311354992765254No Hit
GTATGGAGGTGGGTGTGCAGAGACTGATGAAGGCCATGCACACTGGCTTG3610.14271820862950985No Hit
GTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGGAGTGG3600.14232286733136718No Hit
TATCAGGCCAACGGCTGTGAGAACTTCACTAGGGGGCCAGCTCCGCTTCC3580.1415321847350818No Hit
GTATGTGTATGTGAAGACTGGGAAAAGGAGTGGCGCCCTCTGGGACGTGC3560.14074150213879644No Hit
AGTACATGTAGTGCGCCACAAGCAGAATGATAGCTACTATCAGAGTCAGG3540.13995081954251107No Hit
TACTCAAGGTGGTCCTGATGGCCATCTGTGGCATGAACCCAATAGCTATA3450.13639274785922686No Hit
GCATAAAATGGCATCCCTTTGCCCATGCCAAACAGCACTCCAGCTTGTGT3450.13639274785922686No Hit
GATGTAGAGATTGTAATTAGGGACTCTGATGGGTTGTAGTAAGCGTGAAG3400.13441604136851343No Hit
GCCTTGAAGTTGGCGCCCATCTCTGAGATGTCAGTTGTTATGACAAAGTC3230.12769523930008778No Hit
TTATAAGGCAGCGGCAGCCCAACTGCCGGAGACCCTAGAGACCATTATGC3200.1265092154056597No Hit
TTACAAAAGGAGCCGCACTGAGGAGCGGTGAGGGAAGACTTGATCCATAC3180.12571853280937434No Hit
TCCCAGAGGGCGCCACTCCTTTTCCCAGTCTTCACATACACATACCACGC3160.12492785021308896No Hit
CCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACGTCC3150.12453250891494629No Hit
GGAGTGTACAGAGTGATGACTCGCAGACTGCTAGGTTCAACACAGGTTGG3120.12334648502051822No Hit
GTCTTCCATTATGGTGTTGTTGGTTGTGCCATCAAAGCACCATCTTCTGT3050.12057909593351941No Hit
CCTTAATGGCGATGGCCACACAAGCTGGAGTGCTGTTTGGCATGGGCAAA3040.12018375463537673No Hit
CCTCTGAGCAGCACTAGCATGCGTGACAGGCATGGGCCCAGCCAAGATGA3000.11860238944280596No Hit
CATTAATGGATTTGCTTTGGCCTGGTTGGCAATTCGAGCAATGGCCGTGC2930.11583500035580717No Hit
ACATGTACTTGATCCCAGGCCTACAAGCGGCAGCAGCGCGTGCTGCCCAG2920.11543965905766448No Hit
ACCATGGGATTCTCAATGGACATTGATCTGCGGCCAGCCTCCGCCTGGGC2920.11543965905766448No Hit
GTTGTAGTAAGCGTGAAGTGAAAGTGGCATGGCACATCAAATCAACGATT2910.1150443177595218No Hit
GTATGGATCAAGTCTTCCCTCACCGCTCCTCAGTGCGGCTCCTTTTGTAA2910.1150443177595218No Hit
ATACTGGGGGGATGTCAAGCAGGACTTGGTGTCATACTGTGGGCCTTGGA2880.11385829386509373No Hit
GCTCATACCCGAGCCAGAGAAGCAAAGATCTCCCCAAGATAACCAGATGG2870.11346295256695106No Hit
CTCTAACACCACTAGCTCGAGGCACACTGCTCGTGGCATGGAGAGCGGGC2840.112276928672523No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG2820.11148624607623761No Hit
ATACTTGAGGGGTCTGTGAAGTGGGCTTCATCCATGATGTAGAGATTGTA2780.10990488088366687No Hit
GCTCAGAGGAGAGGACGTATAGGCAGGAACCCTAACAAACCTGGAGATGA2760.1091141982873815No Hit
ATTTCAGGAAGAACTCTCCTGGTTTTTCCGGCTCCTGGATGCAGATCCAA2760.1091141982873815No Hit
GTGCAGGAGGGGTTGAAGAAGAGAATGACCACAAAGATCATCATGAGCAC2740.10832351569109613No Hit
TCTTCTGTCTGTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCC2740.10832351569109613No Hit
GCACTAGCATGCGTGACAGGCATGGGCCCAGCCAAGATGACTCTCTCACC2720.10753283309481074No Hit
CTCATGGGTGGACCATCTTCCTCTACCAAGGAGAAATCACCACTCTCATC2710.10713749179666807No Hit
CACATACACATACCACGCTCCTGCAGCAAAAGGTATAGCTATTGGGTTCA2710.10713749179666807No Hit
CATATCAACAAGGGTTGAAATGGGCGAGGCGGCTGCCATTTTTATGACTG2680.10595146790224No Hit
TTGCCATAGAGTCCTATCACTCTTCCACATTTGTCTAGGATCGGAGATCC2660.10516078530595464No Hit
TCCTGAAATAGTCCGTGAAGCCATAAAAAAGAGACTCCGGACAGTGATCT2660.10516078530595464No Hit
ATTTTATGCATGGGACCTTGGAGTCCCGCTGCTAATGATGGGTTGCTATT2610.1031840788152412No Hit
GGTATGAGCACCACCAGTAATAAAAACACAACAATGAGGACACATGCAAT2600.10278873751709851No Hit
AACTTACACAGACAGAAGATGGTGCTTTGATGGCACAACCAACAACACCA2590.10239339621895581No Hit
CCTCCATACATGTACTCATCTCCAGGTTTGTTAGGGTTCCTGCCTATACG2580.10199805492081314No Hit
GTGTTAGAGCAGCCAAGATTGGTAGAGCGATGTTGTCAGTGCGTGGCACG2560.10120737232452777No Hit
GGCCTGATATGTGCACTGGCCGGAGGGTTTGCCAAGGCAGACATTGAGAT2560.10120737232452777No Hit
GCCTTATAAGGCCTGCTTCCAGTCTCTGCTCGCATGAGCACGGCGAGGTT2560.10120737232452777No Hit
GTGTAAGTTATTCCGGCAGATGCAACCTGATAGGCTAGCCAGACGGGAAG2550.10081203102638508No Hit
ATGGAAGACAGCGTACCAGCAGAGGTGTGGACAAAGTATGGAGAGAAGAG2530.10002134843009972No Hit

[FAIL]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TTTAAAC100.0072367843143.994263
TCAGGTC100.0072367843143.994263
ATAGAAT451.14232535E-895.996183
GAATGGC502.3737812E-886.396566
TAGAATG502.3737812E-886.396564
GAGATAA353.5424157E-582.331271
TCTGTGC353.552859E-582.282432
CATAGAA554.5976776E-878.542332
AGATAAG950.075.8314361
TGGAGAT8550.058.1029475
CTGTGCC502.0776175E-457.5977063
ACTGGAG8400.057.4262853
CTGGAGA8700.057.1011774
CCCAGGA1501.0913936E-1147.998099
TCTGAAC3600.041.998333
CTGAACA3650.041.4230084
TGAACAG3900.038.7676855
GAACAGA3800.037.893236
AACAGAC3850.037.4011047
GGAGATG17300.035.3743136
Produced by FastQC (version 0.11.2)