source: PatientXsomatic_result/PatientXsomatic.0_bwamem.sort.readfiltered.bam | |
QC-passed reads | 458754 |
QC-failed-reads | 0 |
Duplicates | 0 |
Mapped reads | 347409(75.73%) |
Paired reads | 458754 |
Read1 | 229377 |
Read2 | 229377 |
Properly paired | 331618(72.29%) |
Reads with itself and mate mapped | 347388 |
Singletons | 21(0.00%) |
Reads with mate mapped to a different chromosome | 42735 |
Reads with mate mapped to a different chr (mapQ at least 5) | 42735 |
source: PatientXsomatic_result/PatientXsomatic.0_bwamem.sort.readfiltered.bam | |
total length (defined by /auto/rcf-proj/kw/yunfeigu/try_seqmule/somatic/somatic_calling.bed) | 244.59Kb |
Fraction of reads mapped to target region | 41.59% |
Average coverage in target region | 42.59 |
Percentage above 30 | 36.59% |
Percentage above 20 | 43.68% |
Percentage above 10 | 53.56% |
Percentage above 5 | 61.16% |
source: PatientXsomatic_result/PatientXsomatic.0_bwamem.sort.readfiltered.0_varscan.somatic-call.extract.vcf | |
Sample | PatientXsomatic |
Number of variants | 199 |
Number of SNVs | 178 |
Number of indels | 21 |
Transitions | 115 |
Transversions | 63 |
Ti/Tv Ratio | 1.83 |
Ref/Alt heterozygotes | 133 |
Homozygotes | 66 |