FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L003_R2_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L003_R2_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1745479
Sequences flagged as poor quality0
Sequence length75
%GC48

[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

[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

[WARN]Sequence Duplication Levels

Duplication level graph

[WARN]Overrepresented sequences

SequenceCountPercentagePossible Source
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGGGGGGGG48220.2762565461973475Illumina RNA PCR Primer (100% over 50bp)
GGACAGACTGCAGCCATTCGCTCACTGATGAGGAGTAGCAGTGTTGGACGGCTCCCAAGGCGGATGTGGTACAGT32340.18527865416885567Search with Blastn,more detail
First hit on 16: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAAAAAATA30160.17278924581733723Search with Blastn,more detail
First hit on 14: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
GGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGA23960.13726891013870693Search with Blastn,more detail
First hit on 45: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
GGAGAAATATACAGAATGTAGAAAAGTCCTAACAGTCCACTGTGCCCGGGGGTGTAGCCACTTCCTTTCCTTCCC22390.12827424449105373Search with Blastn,more detail
First hit on 16: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
CACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAA21230.12162850426730999Search with Blastn,more detail
First hit on 14: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
CCAGTAAAGACTTAGTGGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAG20090.11509734577156185Search with Blastn,more detail
First hit on 44: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
GCAGTCCCACTTCCAGATGCGCCATGTCCTTGGACTCTCCCTGGGCTCTGAGAGGAAACAGGGTTCTTAAAAGCA19480.11160260306769659Search with Blastn,more detail
First hit on 39: Mus musculus myelin basic protein (Mbp), transcript variant 6, mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
CGGATTGGAAGTTCTATTGGCAGAACGACTCGGTTATCAACTTCTAGCAGTCGTAGTTCACCAGGTTTTAGGTCG19090.10936825937178277Search with Blastn,more detail
First hit on +100: Mus musculus mitochondrial DNA from Lewis lung carcinoma, complete sequence Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGAAA48700.011.73560447
CGTAT33050.011.70748447
CGCGA11450.011.46977857
AACGA55100.010.24539645
GTCGC37850.010.12957742
AAACG56400.09.94600744
CGCCG38200.09.851747544
TTCGC35450.09.41417717
CCGTA41150.09.23176546
ATTCG35150.08.8867116
GGAGA182600.08.7283561
ACGAA67500.08.67862546
CCGTG76350.08.22807326
CGTGG76100.08.16182427
ACGTC69900.08.0414641
CGTCA77500.07.8839982
GCGGA39700.07.780133760
GGCCG78200.07.67032624
GGAAA177400.07.66063931
GCCGT78000.07.64449125

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)