Percentage of uniquely mapped reads

Question

[vivekruhela]

I want to do the alignment assessment means want to check the percentage of mapped reads, unmapped reads, coverage analysis etc. But I don't know how to determine the percentage of uniquely mapped reads from alignment results and variance in depth. Are there any other parameters to assess the alignment results? I want to know how to do it.

Thanks

[Buffo]

Which aligner have you used? Bowtie, HISAT, BWA, etc produces these information by default.

[vivekruhela]

I am using BWA-0.7.17

[GenoMax]

Obtaining uniquely mapped reads from BWA mem alignment (filtering by q score does not seem to do the trick in my case)

[vivekruhela]

Thanks. I'll check it.