FastQCFastQC Report
Wed 21 Sep 2016
cond1rep2_S2_L001_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep2_S2_L001_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences2007025
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC58480.29137653990358864Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG33870.1687572401938192TruSeq Adapter, Index 2 (100% over 63bp)
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT27560.13731767167823022Search 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%
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG27150.13527484709956278Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC24400.12157297492557392Search 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%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC22790.11355115158007498Search 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%
ATTTCGATCTTCCACTATGCCAAGGGACAACCTTACATCGATGAGGTGGGGACCTTCAAAGAGCGCATCCAGTGG21960.10941567743301653Search with Blastn,more detail
First hit on 79: Mus musculus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGTGGGTAGGGGACCCTCGCTGGAAGGATGGCTCCATTGTCATACACAACCTAGACTACAGTGACAACGGCACTT21210.10567880320374683Search with Blastn,more detail
First hit on 78: PREDICTED: Cavia porcellus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA20900.10413422852231537Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TACCTTCTGGTGGCCCAGCTCCACACTCTGTCCTCGGGCTCAAATCCACATCGTGCAGAGCAGACTCTCCATCAG20330.10129420410807041Search 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%

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCGCG19200.011.6483197
CGTAT32200.08.81978645
CGCGG30050.08.3876028
ATACG31800.08.37255670
TCGTA33150.08.1386844
CGTAC33400.07.865189613
CGTCC67800.07.01615322
TAACG37650.06.78877610
ATCGC49350.06.76183566
GCGAT40250.06.703037334
TCGTT61150.06.501978420
ACGTA40400.06.23879812
GCGGT39900.06.2280079
GACGT79500.06.20685520
AATCG47400.06.14128842
CGTTT63700.06.130235721
CGATG94750.05.919728835
TCCGC45000.05.916606435
TTTCG58950.05.901551718
CGACT64350.05.6821496

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)