FastQCFastQC Report
Wed 21 Sep 2016
cond1rep2_S2_L001_R2_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep2_S2_L001_R2_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences2007025
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

[OK]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
GGACAGACTGCAGCCATTCGCTCACTGATGAGGAGTAGCAGTGTTGGACGGCTCCCAAGGCGGATGTGGTACAGT39750.1980543341512936Search with Blastn,more detail
First hit on 16: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGGGGGGGG35770.17822398824130242Illumina RNA PCR Primer (100% over 50bp)
ACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAAAAAATA29950.14922584422216964Search 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%
CCAGTAAAGACTTAGTGGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAG27820.1386131214110437Search 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%
GGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGA27010.13457729724343245Search 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%
CACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAA26190.1304916480860976Search 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%
GGAGAAATATACAGAATGTAGAAAAGTCCTAACAGTCCACTGTGCCCGGGGGTGTAGCCACTTCCTTTCCTTCCC25460.1268544238362751Search 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%
GGGGTTTGTCCCCACACTTTGGTTATCCTATGAGGTTGAGTGGGAGGGAGGTATCTGCTTTCAGATGAAAGGGGG23870.11893225047022334Search with Blastn,more detail
First hit on 70: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
GGCCAAGTGGCCTGGAGTTGGGCAGAGGCTATCAAGGTCCCTTTCTTCTCGGTGTCTGAGAGACAGGCACCAAAC23040.11479677632316489Search with Blastn,more detail
First hit on 30: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
CGGATTGGAAGTTCTATTGGCAGAACGACTCGGTTATCAACTTCTAGCAGTCGTAGTTCACCAGGTTTTAGGTCG22210.11066130217610642Search 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
CGAAA53050.09.36797447
TTCGC36950.09.22273717
ATTCG39950.08.61902216
AACGA59050.08.53633645
GGAGA211750.08.1871531
CGCCG36450.08.08320544
AAACG65600.07.792228744
TACCG24550.07.663504614
GCGGA46600.07.617582360
CGCGA14000.07.606757
GGAAA202750.07.6024651
ACGAC35650.07.468008525
CGTAT37350.07.413223347
ACGGC51750.07.06528948
GTCGC39750.07.054934542
ACGAA73300.07.022101446
ACGTC73300.06.9447951
GGAAG270700.06.825061
CGACT38450.06.73952926
CGTCA79150.06.6436012

[OK]Bad tiles

No bad tiles