FastQCFastQC Report
Wed 11 Jul 2018
mouse_cns_E18_rep1_1.fastq.gz

Summary

[OK]Basic Statistics

MeasureValue
Filenamemouse_cns_E18_rep1_1.fastq.gz
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences750067
Sequences flagged as poor quality0
Sequence length101
%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

[WARN]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

[OK]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGT223492.979600489022981Illumina Paired End PCR Primer 2 (100% over 50bp)
CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCG13110.1747843859281904Illumina Paired End PCR Primer 2 (100% over 31bp)

[OK]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
GAGCGGT40200.060.5775229
AGAGCGG40950.059.352128
AAGAGCG41050.059.0918927
ATCGGAA41850.057.754692
GATCGGA42050.057.615981
TCGGAAG41900.057.4591063
CGGAAGA42000.057.435364
GAAGAGC50000.048.8974656
GGAAGAG55400.044.048535
TACCGCG1300.043.850711
TATGCCG32000.037.8378342-43
CGTATGC32450.037.3812940-41
CTCGTAT31400.037.12178838-39
TCGTATG32250.037.09786240-41
ATGCCGT32850.036.50105744-45
TGCCGTC33200.036.40232544-45
GCCGTCT33100.036.1548446-47
GTATGCC33200.035.96962442-43
CCGTCTT33850.035.70450646-47
AGACCGA33900.035.4975530-31
Produced by FastQC (version 0.11.2)