father

Input Quality Assessment


father.1_phred33
father.2_phred33

Statistics

Alignment stats
source: father_result/father_bwamem.sort.rmdup.readfiltered.bam
QC-passed reads81093904
QC-failed-reads0
Duplicates4395852
Mapped reads72469565(89.36%)
Paired reads81093904
Read140546952
Read240546952
Properly paired79384298(97.89%)
Reads with itself and mate mapped72443713
Singletons25852(0.03%)
Reads with mate mapped to a different chromosome470431
Reads with mate mapped to a different chr (mapQ at least 5)470431


Coverage stats
source: father_result/father_bwamem.sort.rmdup.readfiltered.bam
total length (defined by /home/yunfeiguo/projects/seqmule_parallel/bin/secondary/../../misc/hg19_exome.bed) 46.21Mb
Fraction of reads mapped to target region 53.22%
Average coverage in target region 69.91
Percentage above 3073.03%
Percentage above 2081.25%
Percentage above 1089.25%
Percentage above 593.29%


Variant stats(filter applied)
source: father_result/father.extract_consensus.vcf
Samplefather
Number of variants31184
Number of SNPs29494
Number of indels1690
Transitions21860
Transversions7650
Ti/Tv Ratio2.86
Total heterozygotes18553
Ref/Alt heterozygotes18509
Alt/Alt heterozygotes44
Homozygotes12631


Venn Diagram

Showing overlapping of up to 5 variant output

Coverage Plot

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