father
Input Quality Assessment
father.1_phred33father.2_phred33
Statistics
Alignment stats
source: father_result/father_bwamem.sort.rmdup.readfiltered.bam |
QC-passed reads | 81093904 |
QC-failed-reads | 0 |
Duplicates | 4395852 |
Mapped reads | 72469565(89.36%) |
Paired reads | 81093904 |
Read1 | 40546952 |
Read2 | 40546952 |
Properly paired | 79384298(97.89%) |
Reads with itself and mate mapped | 72443713 |
Singletons | 25852(0.03%) |
Reads with mate mapped to a different chromosome | 470431 |
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 30 | 73.03% |
Percentage above 20 | 81.25% |
Percentage above 10 | 89.25% |
Percentage above 5 | 93.29% |
Variant stats(filter applied)
source: father_result/father.extract_consensus.vcf |
Sample | father |
Number of variants | 31184 |
Number of SNPs | 29494 |
Number of indels | 1690 |
Transitions | 21860 |
Transversions | 7650 |
Ti/Tv Ratio | 2.86 |
Total heterozygotes | 18553 |
Ref/Alt heterozygotes | 18509 |
Alt/Alt heterozygotes | 44 |
Homozygotes | 12631 |
Venn Diagram
Showing overlapping of up to 5 variant output
Coverage Plot