1
$\begingroup$

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?

$\endgroup$
2
  • 1
    $\begingroup$ I haven't touched this subject, hence this is a comment, but for me it is better the second way, However it is much different between method 1 (I think you might want to use the mean instead of add up the percentage) and 2? What do other papers in this field? $\endgroup$
    – llrs
    Commented Sep 15, 2017 at 8:45
  • 1
    $\begingroup$ I wouldn't think either of the options are appropriate. Variants at different sites could be arising from the same mtDNA copy, so I presume one would need to do some sort of LD modelling or something like that to account for this (or accept a relatively crude estimate). $\endgroup$
    – Devon Ryan
    Commented Sep 18, 2017 at 12:18

1 Answer 1

1
$\begingroup$

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.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.