FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L002_R2_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L002_R2_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1716021
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
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGGGGGGGG49650.2893321235579285Illumina RNA PCR Primer (100% over 50bp)
GGACAGACTGCAGCCATTCGCTCACTGATGAGGAGTAGCAGTGTTGGACGGCTCCCAAGGCGGATGTGGTACAGT32060.18682755047869462Search with Blastn,more detail
First hit on 16: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAAAAAATA29130.16975316735634355Search 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%
GGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGA23270.1356044011116414Search 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%
GGAGAAATATACAGAATGTAGAAAAGTCCTAACAGTCCACTGTGCCCGGGGGTGTAGCCACTTCCTTTCCTTCCC22170.12919422314761883Search 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%
CACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAA21190.12348333732512598Search 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%
CCAGTAAAGACTTAGTGGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAG20680.12051134572362458Search 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%
GCAGTCCCACTTCCAGATGCGCCATGTCCTTGGACTCTCCCTGGGCTCTGAGAGGAAACAGGGTTCTTAAAAGCA19680.1146839112108768Search 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%
CGGATTGGAAGTTCTATTGGCAGAACGACTCGGTTATCAACTTCTAGCAGTCGTAGTTCACCAGGTTTTAGGTCG18650.10868165366274656Search 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
CGTAT30100.011.67510347
CGAAA44750.010.15333947
CCGTA36900.09.42739546
CGCGA12900.09.35580557
AACGA47300.09.30577545
CGCCG39650.09.04211844
GTCGC39550.08.70597242
TTCGC35050.08.60840917
ATTCG35950.08.4916416
GGAGA175000.08.4404931
AAACG54450.08.27938144
GCGGA40450.07.546957560
CTAAC61800.07.12238129
GGAAA168850.07.0826531
ACGAA66400.06.842800646
TATAC64100.06.81144248
CGGGG65300.06.7949947
CGTGG72550.06.75201927
TCGGT89550.06.73868836
GCCCG64050.06.70591844

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)