Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-10T06:10:00.103Z
Answers.LastActivityDate: 2018-01-10T06:10:00.103Z
Answers.UserDisplayName: gringer
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-15T08:45:38.863Z
Comments.Text: 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?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-18T12:18:47.290Z
Comments.Text: 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).
Comments.UserDisplayName: Devon Ryan
Tags: <mtdna><heteroplasmy>
Title: Heteroplasmy Calculation
ThreadText: # 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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