mother
Input Quality Assessment
mother.0.0_phred33
mother.0.1_phred33
mother.1.0_phred33
mother.1.1_phred33
Statistics
| source: mother_result/mother_bwamem.merge.bam | |
| QC-passed reads | 3979773 |
| QC-failed-reads | 0 |
| Duplicates | 0 |
| Mapped reads | 3581498(89.99%) |
| Paired reads | 3979773 |
| Read1 | 1989888 |
| Read2 | 1989885 |
| Properly paired | 3890473(97.76%) |
| Reads with itself and mate mapped | 3580331 |
| Singletons | 1167(0.03%) |
| Reads with mate mapped to a different chromosome | 39980 |
| Reads with mate mapped to a different chr (mapQ at least 5) | 39980 |
| source: mother_result/mother_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 | 61.13% |
| Average coverage in target region | 4.22 |
| Percentage above 30 | 0.22% |
| Percentage above 20 | 1.32% |
| Percentage above 10 | 11.32% |
| Percentage above 5 | 35.84% |
| source: mother_result/mother_bwamem.merge.0_samtools.extract.vcf | |
| Sample | mother |
| Number of variants | 4237 |
| Number of SNVs | 4126 |
| Number of indels | 111 |
| Transitions | 2983 |
| Transversions | 1143 |
| Ti/Tv Ratio | 2.61 |
| Ref/Alt heterozygotes | 2876 |
| Homozygotes | 1361 |
Coverage Plot
