Imputation of sequence level genotypes in the Franches-Montagnes horse breed

Table 3 Imputation accuracies on chromosome ECA31 using Impute 2 with different parameter settings

Concordance	SNP number	N_eSHAPEIT	N_eImpute2	Pedigree	rho	Window size	Prephasing with SHAPEIT	Imputation intervall
0.954	129 985	100	100	yes	0.0004²	2 Mb²	all horses	6 Mb²
0.950	128 845	100	100	yes¹	0.0004²	2 Mb²	all horses	6 Mb²
0.953	130 103	100	100	yes¹	0.0004²	2 Mb²	all horses	6 Mb²
0.950	128 501	100	100	no	0.0004²	2 Mb²	all horses	6 Mb²
0.954	130 422	100	100	yes	0.0004²	2 Mb²	all horses	whole ECA31
0.953	130 001	100	100	yes	0.0004²	0.5 Mb	all horses	6 Mb²
0.952	129 511	100	100	yes	0.01	2 Mb²	all horses	6 Mb²
0.953	129 544	15 000²	100	yes	0.0004²	2 Mb²	all horses	6 Mb²
0.971	54 295	100	20 000²	yes	0.0004²	2 Mb²	all horses	6 Mb²
0.956	128 135	100	100	yes	0.0004²	2 Mb²	test pop. only	6 Mb²

The concordance of true and imputed genotypes was calculated with different parameter settings for ECA31; the number of SNPs passing the probability threshold of 0.9 on average per animal is indicated in the second column; Rho: recombination rate in SHAPEIT; the parameters in the first row are the same parameters as in Table 1, except for the quality threshold of 0.9 which was set to 0; ¹only in reference population; ²default value of the software.

ISSN: 1297-9686