father

Input Quality Assessment


father.0.0_phred33
father.0.1_phred33
father.1.0_phred33
father.1.1_phred33

Statistics

Alignment stats
source: father_result/father_bwamem.merge.bam
QC-passed reads3992668
QC-failed-reads0
Duplicates0
Mapped reads3575179(89.54%)
Paired reads3992668
Read11996332
Read21996336
Properly paired3914772(98.05%)
Reads with itself and mate mapped3574162
Singletons1017(0.03%)
Reads with mate mapped to a different chromosome21721
Reads with mate mapped to a different chr (mapQ at least 5)21721


Coverage stats
source: father_result/father_bwamem.merge.bam
total length (defined by /auto/rcf-proj/kw/yunfeigu/Downloads/SeqMule/misc/hg19_exome.bed) 46.21Mb
Fraction of reads mapped to target region 53.28%
Average coverage in target region 3.66
Percentage above 300.12%
Percentage above 200.77%
Percentage above 107.78%
Percentage above 530.53%


Variant stats(filter applied)
source: father_result/father_bwamem.merge.0_samtools.extract.vcf
Samplefather
Number of variants3269
Number of SNVs3203
Number of indels66
Transitions2196
Transversions1007
Ti/Tv Ratio2.18
Ref/Alt heterozygotes2389
Homozygotes880


Coverage Plot

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