FastQCFastQC Report
Wed 21 Sep 2016
cond1rep1_S1_L003_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep1_S1_L003_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1805703
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC53640.29705881864293293Search 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%
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG31910.17671787663862773Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC26350.14592654495229834Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG26040.14420976207050662TruSeq Adapter, Index 1 (100% over 63bp)
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTAGATCGG25040.1386717527744042No hit
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGAGGACCAATGACGTCATGTGG23210.1285371957625368Search 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%
ACACACGACTGATCTCTGGCAGAACTGTACCACATCCGCCTTGGGAGCCGTCCAACACTGCTACTCCTCATCAGT21320.11807035819290326Search 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%
TGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTC21160.11718427670552686Search 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%
TATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACAGATCGGAAGAGCACACGTCTGA20360.11275386926864496Illumina Multiplexing PCR Primer 2.01 (100% over 23bp)
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT18430.10206551132716732Search 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
TTTCG65650.013.08393918
TCGTT67900.013.06857220
CGTTT70700.012.65141221
TCGCG16950.012.1458587
ACGGC77300.011.66401840
CCACG84300.011.24599638
TTCGT84600.010.53079719
CACGG86800.010.39001639
CGGCC89300.010.05603941
ATACG28600.09.92928370
ACCGA71450.09.88737251
CGTCC58600.09.44976422
CGCGG25550.08.89117058
TCCGC35600.08.87700235
GACCG81550.08.83596550
GCGAT37350.08.744102534
CGTAG32100.08.62548566
TTACC105100.08.61206628
CGTAC28700.08.41001813
CGAGG87350.08.25040353

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)