FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L003_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L003_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1745479
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC68070.3899789112329624Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG45520.260788012917944TruSeq Adapter, Index 3 (100% over 63bp)
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG29220.16740390460154492Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTC27340.15663322216996023Search 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%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC22180.12707113634710016Search 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%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA19360.11091511269972311Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TTAGGTTGCTGAGTATTTTTTATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGA18960.10862347813981148Search 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%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC18880.10816515122782915Search with Blastn,more detail
First hit on +100: PREDICTED: Chinchilla lanigera secreted protein, acidic, cysteine-rich (osteonectin) (Sparc), transcript variant X4, mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGA18710.10719120653986672Search with Blastn,more detail
First hit on +100: Homo sapiens clone LA13_165F6 sequence Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAA18140.10392562729199263Search with Blastn,more detail
First hit on +100: Homo sapiens clone LA13_165F6 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
TCGCG16850.014.1132687
CGTAT32800.011.68732245
TCGTA32950.011.20322344
ATACG27100.010.48088170
CGTCC61750.010.00206822
CGCGG26350.09.9679028
CTAGG74200.08.46879450
GCCGT48950.08.26807450
GCGAT37350.08.17307234
TACGG35850.08.0218271
TATAT116750.07.9981291
CCTAG84700.07.87842749
TCTCG49150.07.87146642
ATCGC43050.07.75320966
CGTAC28250.07.6643713
CGTTT56800.07.498907621
GACGT82100.07.39295520
TATTA89400.07.3081453
AATCG41950.07.27644257
TTTCG56300.07.250691418

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)