FastQCFastQC Report
Wed 21 Sep 2016
cond1rep1_S1_L004_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep1_S1_L004_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1788497
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

[FAIL]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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC52840.29544360432251215Search 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%
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG32500.18171682703409625Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTAGATCGG26120.1460444160655567No hit
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG25700.14369607553157762TruSeq Adapter, Index 1 (100% over 63bp)
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC25090.1402853904703223Search with Blastn,more detail
First hit on 55: Mus musculus myelin basic protein (Mbp), transcript variant 6, mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTCATGTGG23760.1328489787793885Search with Blastn,more detail
First hit on 15: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACAGATCGGAAGAGCACACGTCTGA20990.11736111382909785Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACACACGACTGATCTCTGGCAGAACTGTACCACATCCGCCTTGGGAGCCGTCCAACACTGCTACTCCTCATCAGT20370.11389451589798585Search with Blastn,more detail
First hit on 18: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pmp22:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTC19980.11171391397357669Search with Blastn,more detail
First hit on +100: PREDICTED: Cavia porcellus collagen alpha-1(I) chain-like (LOC100717127), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT19000.10623445272762548Search with Blastn,more detail
First hit on 13: Mus musculus targeted non-conditional, lacZ-tagged mutant allele Pcp4l1:tm1e(KOMP)Wtsi; transgenic Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%

[FAIL]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCGCG16400.015.368377
TTTCG59150.012.48343418
TCGTT65300.011.68828320
CGCGG24650.011.2328778
CGTTT67500.011.04437121
ACGGC75950.010.23598540
CCACG82950.09.62896238
ACCGA66900.09.55177251
CGTCC60550.09.49787222
CACGG83250.09.21049139
TTCGT81500.09.1036219
CGTAC28150.09.07961413
CGGCC86700.08.96681741
ATACG27300.08.84218470
CGTAG29300.07.9963166
GCGAT36100.07.86698334
TTACC104100.07.74127928
ATCGC38450.07.6629336
TCCGC34950.07.61776135
CGAGG80750.07.60573553

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)