FastQCFastQC Report
Wed 21 Sep 2016
cond1rep3_S3_L004_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep3_S3_L004_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1724996
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC65960.3823776982671264Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG47850.2773919475755306TruSeq Adapter, Index 3 (100% over 63bp)
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG29740.1724061968839348Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGACGTGCAAATCGGTCGTCCGACCTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTC26450.15333368888971335Search 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%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC20590.11936259562341014Search 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%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA19550.1133335961358751Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TTAGGTTGCTGAGTATTTTTTATTTGCCCATCCATTCTTTCGTTTGTTTACCTGAGCCCACGGCCCCATGACCGA18670.10823213503103775Search 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%
TTGTTGGTTTTCGGAACTGAGGCCATGATTAAGAGGGACGGCCGGGGGCATTCGTATTGCGCCGCTAGAGGTGAA18240.1057393756275377Search with Blastn,more detail
First hit on +100: Homo sapiens clone LA13_165F6 sequence Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGACGGACCAGAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGA17920.10388429886214229Search with Blastn,more detail
First hit on +100: Homo sapiens clone LA13_165F6 sequence Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC17880.10365241426646787Search 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%

[WARN]Adapter Content

Adapter graph

[FAIL]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TCGCG17950.015.0302367
CGTAT32750.013.44085945
TCGTA35350.012.3518644
CGCGG26500.011.2525278
CGTCC64100.010.30081522
GCCGT48150.09.80555250
TATAT109250.09.1002641
ATACG27350.08.82608870
TCTCG51750.08.7804442
CTAGG77300.08.49589150
GACGT79450.08.35534520
TGCCG57100.08.14426449
TATTA88950.08.1419053
CCGTC62350.07.97137851
CCTAG85200.07.87478849
GCGAT34850.07.84340534
ATCGC42450.07.77717546
GCGGT37950.07.7639549
CTCGT60550.07.62159543
TAGGC64550.07.589260636

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)