Hi,

I am using the bam-readcount tool to compute the statistics of variants detected from NGS. I have one question. How is the "average position on the read" is calculated and how is it different from "the distance to the 3' end of the read"? Please see the attached for a snapshot of T>C mutation in the TP53 gene. It seems to me that the average position of the variant is ~0.5. I also get similar number by looking at the MD tag of the bam file. But, bam-readcount provides 0.98 for that metric. For distance to 3', it provides 0.49. I am probably missing something here. An explanation will be appreciated.

igv-snapshot

Thanks, Rahul