PatientXsomatic

Input Quality Assessment

Alignment stats
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

Coverage stats
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%

Variant stats(filter applied)
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