FastQCFastQC Report
Thu 22 Feb 2018
HVHNVAFXX_n01_female_transmission_spinal_cord_pcr1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
FilenameHVHNVAFXX_n01_female_transmission_spinal_cord_pcr1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences433779
Sequences flagged as poor quality0
Sequence length150
%GC49

[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
GAATGGTTTTGGCGATACTAGCCTTTTTGAGATTTACAGCAATCAAGCCA16460.3794558980494676No Hit
GTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCAGGCAATGGCAA12090.27871335403511927No Hit
CTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTA11490.264881425795163No Hit
GTATTACCTGACCATGAACAATAAGCATTGGTTGGTGCACAAAGAGTGGT11450.26395929724583256No Hit
ATGCTGGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGCAACAC10610.24459459770989375No Hit
GGTAATACAGATCTGAAAAGTCAAGGCCTGTCCTTGGTTCACAGTCAAGT10550.2432114048858981No Hit
GAGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCG9150.21093690565933346No Hit
TCCTTGTAGAGTGAGAAGGGAGCGTCACGGCTCTTCTAGATCGCCGTGCC8620.19871870238070535No Hit
ATCTAAGCTTGTCCATTTTTAGGCGGCATTTCAAATGGCCAGAGAACAGC8270.19065007757406421No Hit
AGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGGATTTG8020.18488677414074908No Hit
GAATATGACACGCCCTTCAATCTAAGCTTGTCCATTTTTAGGCGGCATTT7810.1800455992567644No Hit
TAATAAAGAAGTTCAAGAAAGATCTTGCTGCCATGTTGAGAATAATCAAT7460.17197697445012322No Hit
TTCATATCCTGTATCATTGACAATCATCCCGCTATGCTGGGAGCCATGCA7440.17151591017545803No Hit
CATATTGAGTGTCTGATTGCTTGTCAAGGTAGGCTTCACCTTGTGTTGGG7400.1705937816261276No Hit
GTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGCATAGGAGTGG7370.16990218521412978No Hit
GTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAAATCC7370.16990218521412978No Hit
TCTTAGAACACGTAAACTTGGCACATGTCACCAAGCTCCCTTTGCCAAAA7080.16321675323148424No Hit
GTTAGTAACATGGCCGAGGTAAGATCCTATTGCTACGAGGCATCGATATC7030.1620640925448212No Hit
GTTCGAGTCTGAAGCGAGAGCTAACAACAGTATCAACAGGTTTAATTTGG6970.16068089972082558No Hit
CTCAATATGTCTGCAAAAGAACATTAGTGGACAGAGGTTGGGGAAACGGT6830.1574534497981691No Hit
TCCGTACACAACCCAAGTTGATGTCGTGTTGCACCAGCAATCGACATCAT6760.1558397248368409No Hit
GTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTGTAGTCA6590.1519206785021866No Hit
CCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGA6550.15099854995285616No Hit
GTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGTATCAG6470.14915429285419535No Hit
ACTCTATGTCAACTGTTGGCTTGTCCTGTGCCATCACGGTAACGCAGCCT6470.14915429285419535No Hit
GTACAGATCATGGACCTCGGGCACATGTGTGACGCCACCATGAGTTATGA6450.14869322857953013No Hit
TCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAAA6340.14615737506887147No Hit
CTACAAGGAAGTTGCAAACGCGGTCGCAGACCTGGTTAGAATCAAGAGAA6330.14592684293153887No Hit
GGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATTGGGAG6320.14569631079420628No Hit
GTATCAACAGGTTTAATTTGGATTTGGAAACGAGAGTTTCTGGTCATGAA6310.14546577865687366No Hit
GCATACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTT6300.14523524651954106No Hit
CTCCAAGAGAGAAGTGGTCCATATGATCGGTTGACCCCGCTGTCACCATT6260.14431311797021062No Hit
GTCTTTAGCTGGTCCACTCAGCCACCACAACACCAGAGAGGGTTACAGAA6230.1436215215582128No Hit
GTCATATTCCTTGTGCACTGCGGCATTCACATTCACCAAGGTCCCAGCTG6150.141777264459552No Hit
ATCATGACCAAGTATATGACTTTTTGGCTCGTCGAGCTTCCCAAAAGCCA6080.14016353949822374No Hit
CTTCTAGATCGCCGTGCCTCACCTTTTTTGTGATGACAGGTTCCGTACAC5990.1380887502622303No Hit
GTCATGGACCCATCAGAATGGTTTTGGCGATACTAGCCTTTTTGAGATTT5920.13647502530090208No Hit
GCTAAAGACTTGGGTATGATAAGATCACTTTCTTCTACTCCATCTGTCCA5900.13601396102623686No Hit
GATCTGTACGTGGCACTTGTTCACTCCCAATGTGGTAGCAAACGAAATGG5880.13555289675157164No Hit
TCCCTTAACAGCTGTTCCTATGACGGCTGGGTCACATTCTAATGAGTAAT5740.1323254468289152No Hit
ATCTAGAAGAGCCGTGACGCTCCCTTCTCACTCTACAAGGAAGTTGCAAA5670.13071172186758695No Hit
GTACATGTAGTATGCACTCCCGCGTCTAGTGATCTCTGCTGCCATGGCTG5640.13002012545558914No Hit
TACTACATGTACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGC5620.12955906118092392No Hit
GGATATGAAACTGACGAAAATAGAGCGAAAGTCGAGGTTACGCCTAATTC5590.1288674647689261No Hit
TTCTTACATTGTCATAGGAGTTGGGGACAAGAAAATCACCCACCACTGGC5580.1286369326315935No Hit
GTACAAGTACCATCCTGACTCCCCCCGCAGATTGGCAGCAGCAGTCAAGC5580.1286369326315935No Hit
CTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTTTTG5570.12840640049426089No Hit
TACTTGGATAGGAGCGATGCCGGGAAGGCCATTTCGTTTGCTACCACATT5510.1270232076702653No Hit
ATATCGGACATGGCTTCGGACAGTCGTTGCCCAACACAAGGTGAAGCCTA5480.12633161125826745No Hit
ATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATGACTTT5470.12610107912093485No Hit
CTCATAACTCATGGTGGCGTCACACATGTGCCCGAGGTCCATGATCTGTA5450.12564001484626966No Hit
AGTTATGAGTGCCCTATGCTGGATGAGGGAGTGGAACCAGATGATGTCGA5350.1233346934729436No Hit
AGCTTAGATTGAAGGGCGTGTCATATTCCTTGTGCACTGCGGCATTCACA5250.12102937209961753No Hit
TTCCAAGACAACATCAACCCAGGTCCCACCTGACATGCCCTCCACGAAGT5230.12056830782495233No Hit
GTTGAGAATAATCAATGCTAGGAAAGAGAGGAAGAGACGTGGCGCAGACA5220.12033777568761975No Hit
TCCATGCTCTGTGCTCAAGCGGACATTCCTTCAGTGTGTCACCGTCGACA5210.12010724355028712No Hit
CATTGGGAGTGAACAAGTGCCACGTACAGATCATGGACCTCGGGCACATG5150.11872405072629151No Hit
GTTACTAACCGTCGTCGTGACCAACTCTATGTCAACTGTTGGCTTGTCCT5150.11872405072629151No Hit
TTCCTTCAGTGTGTCACCGTCGACAACAAAACTGTTGTTGGTCTTTGCCG5040.11618819721563285No Hit
GTCAGTGCGTGGCACGGCCATTGCTCGAATTGCCAACCAGGCCAAAGCAA5030.11595766507830024No Hit
GTATCAGGTGCATTGGAGTCAGCAATAGAGACTTCGTGGAGGGCATGTCA5020.11572713294096762No Hit
CACTAGCAGCGTGCCTATGAGGATCTGTGAGAACCAGGACATTCCTCCAA4920.1134218115676416No Hit
ATTCTAACCAGGTCTGCGACCGCGTTTGCAACTTCCTTGTAGAGTGAGAA4920.1134218115676416No Hit
GTCTCACACATTGTGGACAGATGGAGTAGAAGAAAGTGATCTTATCATAC4910.11319127943030897No Hit
ATCCTAGAGGAGAATGGAGTTCAACTGACAGTTGTTGTGGGATCTGTAAA4870.11226915088097857No Hit
ACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTG4870.11226915088097857No Hit
ATCCAGCATAGGGCACTCATAACTCATGGTGGCGTCACACATGTGCCCGA4860.11203861874364594No Hit
ACCTGATACTGTATGCCGGGGCAATCAGCAGTATCATGACCAAGTATATG4840.11157755446898074No Hit
TTATAGATGAATACCCCCGTGCCACATCTCGTTTCCTTTTTTGAGAAGTC4810.11088595805698294No Hit
GGATGAGGGAGTGGAACCAGATGATGTCGATTGCTGGTGCAACACGACAT4740.1092722330956547No Hit
GGGTAAGGGCATTCACCAGATTTTTGGAGCAGCCTTCAAATCACTGTTTG4690.10811957240899168No Hit
GGCCTGGGAAGAGGGGATCTGTGGGATCTCATCCGTTTCAAGAATGGAAA4670.10765850813432647No Hit
TTAGTGGACAGAGGTTGGGGAAACGGTTGTGGACTTTTTGGCAAAGGGAG4660.10742797599699386No Hit
TCCTTGAATTCTACCAATGCCTCTTTGTTGTTCCAGTGTGGAGTTCCGGT4580.10558371889833303No Hit
CTCACGGGGTGTCCAATTGGCTCTGAAAATGAAGGAGACCAGCAAGGCTG4490.10350892966233959No Hit
CTCTTGGAGTGCTTGTGATTCTACTCATGGTGCAGGAGGGGTTGAAGAAG4380.10097307615168091No Hit
CTCTTGATTCTAACCAGGTCTGCGACCGCGTTTGCAACTTCCTTGTAGAG4380.10097307615168091No Hit

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TAATCAG100.007235841144.012332
CAGTGCG800.0107.9967963
AGTGCGT850.0101.644044
GTCAGTG1050.082.292761
GTTCGAG1350.080.006851
TTCGAGT1450.079.455082
TCGAGTC1500.076.797733
CGAGTCT1550.074.320384
TGCGTGG1950.073.852482
GCGACAG300.00198818172.006171
GTGCGTG2000.072.006171
ACAGTTC608.416646E-871.997863
GCGTGGC2200.068.7252353
CGACAGT554.2257107E-665.460151
AGTTCGA607.085142E-659.9982225
GAGTCTG2050.056.1934555
ATGTGTA400.006217187353.9983988
AGTCTGA2500.051.8444371
CAGTTCG701.7655133E-551.4270444
AAATTTT1301.4006218E-1049.8446775
Produced by FastQC (version 0.11.2)