source: father_result/father_bwamem.merge.bam | |
QC-passed reads | 3992668 |
QC-failed-reads | 0 |
Duplicates | 0 |
Mapped reads | 3575179(89.54%) |
Paired reads | 3992668 |
Read1 | 1996332 |
Read2 | 1996336 |
Properly paired | 3914772(98.05%) |
Reads with itself and mate mapped | 3574162 |
Singletons | 1017(0.03%) |
Reads with mate mapped to a different chromosome | 21721 |
Reads with mate mapped to a different chr (mapQ at least 5) | 21721 |
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 30 | 0.12% |
Percentage above 20 | 0.77% |
Percentage above 10 | 7.78% |
Percentage above 5 | 30.53% |
source: father_result/father_bwamem.merge.0_samtools.extract.vcf | |
Sample | father |
Number of variants | 3269 |
Number of SNVs | 3203 |
Number of indels | 66 |
Transitions | 2196 |
Transversions | 1007 |
Ti/Tv Ratio | 2.18 |
Ref/Alt heterozygotes | 2389 |
Homozygotes | 880 |