FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L004_R2_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L004_R2_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1724996
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
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAGGGGGGGGGG50470.2925803885922054Illumina RNA PCR Primer (100% over 50bp)
GGACAGACTGCAGCCATTCGCTCACTGATGAGGAGTAGCAGTGTTGGACGGCTCCCAAGGCGGATGTGGTACAGT32140.1863192726244003Search with Blastn,more detail
First hit on 16: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAAAAAATA30070.1743192447982488Search 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%
GGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGA22910.13281190217252678Search 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%
GGAGAAATATACAGAATGTAGAAAAGTCCTAACAGTCCACTGTGCCCGGGGGTGTAGCCACTTCCTTTCCTTCCC22760.13194233493874769Search 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%
CACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAGGTAAACAAACGAAAGAATGGATGGGCAAATAA21170.12272492226068929Search 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%
CCAGTAAAGACTTAGTGGGGAACTGCAAAAGCCACATGACGTCATTGGTCCTCGGTCATGGGGCCGTGGGCTCAG20110.11657998047531705Search 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%
GCAGTCCCACTTCCAGATGCGCCATGTCCTTGGACTCTCCCTGGGCTCTGAGAGGAAACAGGGTTCTTAAAAGCA19580.11350750958263091Search 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%
CGGATTGGAAGTTCTATTGGCAGAACGACTCGGTTATCAACTTCTAGCAGTCGTAGTTCACCAGGTTTTAGGTCG19410.1125220000510146Search 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
CGTAT32200.013.78411847
CCGTA37900.011.61499846
CGCCG39650.011.10139144
GTCGC42750.010.71124542
CGAAA47550.010.60382847
AACGA52800.09.6142145
CGCGA12750.09.46575157
GGAGA183650.08.8433231
AAACG58750.08.3985844
TCGCC57050.08.27551343
TCGGT94100.07.61899536
ACGAA67750.07.54553246
GTATC66150.07.461435348
TACCG21900.07.455466714
TTCGC33600.07.394474517
GAACG83500.07.268934723
GGTCG66550.07.253152441
ATTCG35250.07.249731516
ACGTC68850.07.22627261
CGGTG72250.07.221300637

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)