<p>Heteroplasmy at <em>any</em> 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.</p>

<p>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.</p>

CC BY-SA 3.0
2018-01-10T06:10:00.103Z
2018-01-10T06:10:00.103Z
gringer
<p>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?</p>

CC BY-SA 3.0
2017-09-15T08:45:38.863Z
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?
llrs
CC BY-SA 3.0
2017-09-18T12:18:47.290Z
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).
Devon Ryan
<mtdna><heteroplasmy>
Heteroplasmy Calculation
# Heteroplasmy Calculation

(Asked by: username_0 on 2017-09-14)

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?

**Tags:** mtdna, heteroplasmy
> **Comments:**
> **username_1**: 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?  
> **username_2**: 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).  

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## 1 answers

### Answer by username_3 on 2018-01-10. Score: 1 | Accepted answer

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.


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