FastQCFastQC Report
Wed 21 Sep 2016
cond1rep2_S2_L002_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep2_S2_L002_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences1996979
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC58670.29379377549788954Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG33910.16980649270723427TruSeq Adapter, Index 2 (100% over 63bp)
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG28290.14166398344699668Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT27190.1361556631291566Search 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%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC23990.12013145856816722Search 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%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC23320.11677639073821007Search 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%
ATTTCGATCTTCCACTATGCCAAGGGACAACCTTACATCGATGAGGTGGGGACCTTCAAAGAGCGCATCCAGTGG21320.10676126288759172Search with Blastn,more detail
First hit on 79: Mus musculus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA20540.10285536302585055Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TACCTTCTGGTGGCCCAGCTCCACACTCTGTCCTCGGGCTCAAATCCACATCGTGCAGAGCAGACTCTCCATCAG20500.10265506046883818Search 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
TCGCG19500.010.9229547
CGTAT29850.09.15735145
CGTAC32100.08.18370813
TCGTA33000.08.17566644
ATACG29850.07.730231370
TAACG35900.07.71300510
CGCGG30300.07.4982658
CGTCC71100.07.239721322
CGATC38950.06.6533275
ACGTA39550.06.6421512
TCGTT61400.06.591130320
TATAT133100.06.43295531
TTTCG59800.06.411298818
GACGT81400.06.410861520
TACGG44200.06.26463571
CGTTT66150.06.171509721
CTAGG90650.06.148303550
GTCCG38300.06.11742418
GCGAA36850.06.06913137
GGTCG38850.06.0308214

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)