FastQCFastQC Report
Wed 21 Sep 2016
cond1rep2_S2_L003_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep2_S2_L003_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences2031272
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC59630.2935598974435723Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG33530.16506898140672444TruSeq Adapter, Index 2 (100% over 63bp)
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG28160.13863234465891322Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT28150.1385831144228838Search 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%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC24970.12292789936552073Search 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%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC23350.11495260112875086Search 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%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA21460.105648086519186Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ATTTCGATCTTCCACTATGCCAAGGGACAACCTTACATCGATGAGGTGGGGACCTTCAAAGAGCGCATCCAGTGG21320.1049588632147738Search with Blastn,more detail
First hit on 79: Mus musculus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGTGGGTAGGGGACCCTCGCTGGAAGGATGGCTCCATTGTCATACACAACCTAGACTACAGTGACAACGGCACTT20330.10008506984785888Search with Blastn,more detail
First hit on 78: PREDICTED: Cavia porcellus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCGCG20450.010.5874837
CGTAT30700.08.32455545
CGCGG29200.08.1441968
TCGTA31550.07.987776344
CGTCC72600.07.284423422
TTTCG61900.07.22514918
ATACG31900.07.121600670
TCGTT64850.06.95087220
CGATC40700.06.7190715
TATAT126350.06.63311531
CGTTT65750.06.585816421
GACGT81950.06.1934520
CGTAC34350.06.09681313
ACGGC77350.06.057618640
TCCGC42150.05.981196435
GCGGT41250.05.937059
TACGG45450.05.857257462
CTAGG88750.05.83917450
CACGG84900.05.812597339
GCGAT42800.05.8065434

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)