example
Input Quality Assessment
example.0example.1
Statistics
Alignment stats
source: example_result/example.0_bwamem.sort.rmdup.readfiltered.bam |
QC-passed reads | 294058 |
QC-failed-reads | 0 |
Duplicates | 0 |
Mapped reads | 201139(68.40%) |
Paired reads | 294058 |
Read1 | 144504 |
Read2 | 149554 |
Properly paired | 167300(56.89%) |
Reads with itself and mate mapped | 201118 |
Singletons | 21(0.01%) |
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: example_result/example.0_bwamem.sort.rmdup.readfiltered.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 | 12.83% |
Average coverage in target region | 0.04 |
Percentage above 30 | 0.03% |
Percentage above 20 | 0.05% |
Percentage above 10 | 0.09% |
Percentage above 5 | 0.16% |
Variant stats(filter applied)
source: example_result/example.0_bwamem.sort.rmdup.readfiltered.realn.0_gatklite.extract.vcf |
Sample | example |
Number of variants | 54 |
Number of SNVs | 52 |
Number of indels | 2 |
Transitions | 24 |
Transversions | 28 |
Ti/Tv Ratio | 0.86 |
Ref/Alt heterozygotes | 27 |
Homozygotes | 27 |
Venn Diagram (SNV)
Showing overlapping of up to 5 SNV variant output
Venn Diagram (non-SNV)
Showing overlapping of up to 5 NON-SNV variant output
Coverage Plot