FastQCFastQC Report
Wed 21 Sep 2016
cond1rep2_S2_L004_R1_001.fastq.bz2

Summary

[OK]Basic Statistics

MeasureValue
Filenamecond1rep2_S2_L004_R1_001.fastq.bz2
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences2013421
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
TATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCC56840.28230558834938146Search 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%
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAG34190.16981048672880633TruSeq Adapter, Index 2 (100% over 63bp)
TCTAGAGTGTTCTGTGCCTCCAAGGACTGTCTGGCGATGACTTGTATTGGCCACCAACTGTAGATGTATATACGG27940.13876879202114212Search with Blastn,more detail
First hit on 76: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
ACTAAGTCTTTACTGGAGAGCCAGGCAGGCAAGCAGCGCATAATCGATGCCCTCTGACCACTACGGAGCACAGTT27450.13633512315606125Search 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%
TTATCCCTCTAACGTACTATGTCTTTTGATTTAGCATGCCTTCTGTAGACCTTCCAAAGAGCCCCACACTGGCAC24380.12108744271565658Search 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%
AATGACAACAAGACCTTCGACTCTTCCTGCCACTTCTTTGCCACCAAGTGCACCCTGGAGGGCACCAAGAAGGGC23120.11482943706259147Search 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%
ATTTCGATCTTCCACTATGCCAAGGGACAACCTTACATCGATGAGGTGGGGACCTTCAAAGAGCGCATCCAGTGG21270.10564109542912288Search with Blastn,more detail
First hit on 79: Mus musculus myelin protein zero (Mpz), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
TGCACATCGCGGTGCTAGTGTTGCTCTTCGTCTCCACCATCGTCAGCCAATGGCTCGTGGGCAATGGACACACGA20700.10281009287178389Search with Blastn,more detail
First hit on +100: Mus musculus peripheral myelin protein 22 (Pmp22), mRNA Evalue=3.3219e-33, Ident=100%, QueryCovergap=0%
AGTGGGTAGGGGACCCTCGCTGGAAGGATGGCTCCATTGTCATACACAACCTAGACTACAGTGACAACGGCACTT20510.1018664253526709Search 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
TCGCG20100.010.243527
TCGTA30950.08.83176144
CGTAT31150.08.66109645
CGTCC70350.07.670024422
CGCGG29300.07.6329118
ATACG30400.07.590454670
TTTCG61200.07.308818318
TCGTT65350.06.790186420
CGTTT68100.06.568114321
CGATC38950.06.3806045
GCGAT42900.06.371632634
TATAT130450.06.37016731
GACGT79850.06.224011420
CCACG86250.06.132596538
CGTAC34300.06.002762313
TCCGC45200.05.890336535
ATCGC48600.05.8434726
TACGG43400.05.807599571
CGATG95150.05.782826435
TTCGT81300.05.763833519

[OK]Bad tiles

No bad tiles

Produced by FastQC (version 0.11.5)