Heteroplasmy Calculation For calculating heteroplasmy in mtDNA I was using MitoSeek, the tool provides position wise heteroplasmy percentage. So, will it be wise to add up all sites to get a position-wise percentage in a single sample, or calculate it by adding up all counts (variants) from an aligned file and divide it by total read count?
Heteroplasmy at any site (as long as it's a reliable variant) suggests that there is mitochondrial heteroplasmy, it doesn't matter where it is. In that case, the "mitochondrial heteroplasmy" statistic would simply be the maximum value at any [reliable] location.

Due to the low amount of variation in the mitochondrial genome, and because it's a haploid genome, I don't think that a calculation like "average heteroplasmy" makes much sense for mitochondria.