FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L001_R2_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L001_R2_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1722801
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
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGGGGGGGG48460.28128611487919963Illumina RNA PCR Primer (100% over 50bp)
GGACAGACTGCAGCCATTCGCTCACTGATGAGGAGTAGCAGTGTTGGACGGCTCCCAAGGCGGATGTGGTACAGT33110.19218702566343995Search with Blastn,more detail
First hit on 16: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAAAAAATA30620.17773381835743074Search 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%
GGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGA23030.13367765632827006Search 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%
GGAGAAATATACAGAATGTAGAAAAGTCCTAACAGTCCACTGTGCCCGGGGGTGTAGCCACTTCCTTTCCTTCCC21860.12688639024472356Search 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%
CACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAA21310.1236939147353641Search 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%
CCAGTAAAGACTTAGTGGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAG21170.12288128460570895Search 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%
CGGATTGGAAGTTCTATTGGCAGAACGACTCGGTTATCAACTTCTAGCAGTCGTAGTTCACCAGGTTTTAGGTCG19530.11336190308689163Search 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%
GCAGTCCCACTTCCAGATGCGCCATGTCCTTGGACTCTCCCTGGGCTCTGAGAGGAAACAGGGTTCTTAAAAGCA19070.1106918326608819Search 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%

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
CGCGA11850.013.18054657
CGAAA47750.010.63069647
CGTAT32800.09.74019647
AACGA55350.09.36341645
GTCGC36150.09.23035942
AAACG60000.08.69691444
CCGTA38600.08.64449546
TTCGC32600.08.602180517
CCGCG19000.08.40732856
CGCCG38450.08.40125444
GGAGA183050.08.1905441
CCGTG73350.08.03354126
GGAAA174400.07.55536841
ACGAA67500.07.52023446
GGCCG72950.07.493668624
ATTCG36100.07.473180316
CGTGG74650.07.46567227
CGCAA23650.07.354683432
CGTCA75650.07.32856942
ATACG22850.07.301476536

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)