mother
Input Quality Assessment
mother.1_phred33
mother.2_phred33
Statistics
| source: mother_result/mother_bwamem.sort.rmdup.readfiltered.bam | |
| QC-passed reads | 71205444 |
| QC-failed-reads | 0 |
| Duplicates | 10487284 |
| Mapped reads | 64073406(89.98%) |
| Paired reads | 71205444 |
| Read1 | 35602722 |
| Read2 | 35602722 |
| Properly paired | 69591070(97.73%) |
| Reads with itself and mate mapped | 64049764 |
| Singletons | 23642(0.03%) |
| Reads with mate mapped to a different chromosome | 711928 |
| Reads with mate mapped to a different chr (mapQ at least 5) | 711928 |
| source: mother_result/mother_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 | 61.07% |
| Average coverage in target region | 63.76 |
| Percentage above 30 | 65.64% |
| Percentage above 20 | 73.85% |
| Percentage above 10 | 82.78% |
| Percentage above 5 | 88.92% |
| source: mother_result/mother.extract_consensus.vcf | |
| Sample | mother |
| Number of variants | 31021 |
| Number of SNPs | 29411 |
| Number of indels | 1610 |
| Transitions | 21778 |
| Transversions | 7642 |
| Ti/Tv Ratio | 2.85 |
| Total heterozygotes | 18461 |
| Ref/Alt heterozygotes | 18423 |
| Alt/Alt heterozygotes | 38 |
| Homozygotes | 12560 |
Venn Diagram
Showing overlapping of up to 5 variant output
Coverage Plot
