Question: Need some help interpreting Michigan Server Imputation output statistics
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gravatar for Volka
8 months ago by
Volka40
Volka40 wrote:

Hi all, I have just performed imputation on a chromosome X dataset, using the Michigan Imputation server, and I am a bit confused about the output statistics.

Here are the output statistics at pastebin : https://pastebin.com/S9QG7eX1

Am I right in thinking that here, "Match" indicates the number of SNPs that match on the reference genome? If so, then I am wondering why is it that the remaining sites to be imputed have somewhat doubled from 34,455 SNPs to 66,049?

Thanks very much!

ADD COMMENTlink modified 8 months ago • written 8 months ago by Volka40

34,455 SNPs equates to 68,910 alleles (34,455 * 2). There is then some filtering occurring. I note that you have males in your data, though (1 chrX). For a better response, you may consider contacting Michigan Imputation Server help / support.

ADD REPLYlink written 7 months ago by Kevin Blighe39k
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