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Table 3 Imputation accuracy of the MNEc670k SNP genotyping array

From: Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

Tagging Group

670 K to 2 M

Num Imputed Samples

Land Race

0.981 +/− 0.001

3

Arabian

0.993 +/− 0.0009

13

Belgian

0.992 +/− 0.0005

7

Draft

0.9658 +/− 0.0140

6

F. Montange

0.988 +/− 0.0017

10

Icelandic

0.989 +/− 0.0012

6

Lusitano

0.992 +/− 0.0004

7

Maremanno

0.994 +/− 0.0005

9

Morgan

0.988 +/− 0.0036

20

Pony

0.991 +/− 0.0025

19

Quarter Horse

0.983 +/− 0.0033

25

Standardbred

0.989 +/− 0.0045

13

Thoroughbred

0.991 +/− 0.0068

9

Warmblood

0.985 +/− 0.0116

9

Trotter

0.9857 +/− 0.0046

9

  1. Breed specific imputation accuracy (mean +/− s.e.m.) of genotypes from MNEc670k to MNEc2M SNP sets. In each tagging breed group, 1/3 of samples genotypes were masked to lower density SNP sets and removed from the reference population of 485 horses. Imputation was performed using Beagle 4.0 and concordance was determined with VCFtools
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BMC Genomics

ISSN: 1471-2164

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