Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population

Table 1 Imputation scenarios with HD genotypes using different groups of purebred and crossbred animals

Scenario^a	Number of reference animals^b	Number of imputed animals	Description of reference animals	Density of reference panel^c	Imputed group breed^d	Density of panel of imputed animals
1_5K50K	500	116	Romney	50K	Romney	5K
1B_5KHD_1STEP	500	116	Romney	HD	Romney	5K
1B_5KHD_2STEP	17,000 + 500	116	Romney	HD	Romney	5K
2_50KHD	500	116	Romney	HD	Romney	50K
3_5K50K	469	116	Romney-31 animals related with the imputed group	50K	Romney	5K
3B_5KHD	469	116	Romney-31 animals related with the imputed group	HD	Romney	5K
4_50KHD	469	116	Romney-31 animals related with the imputed group	HD	Romney	50K
5_5K50K	500 (R) + 100 (P)	116	Romney + Perendale	50K	Romney	5K
5B_5KHD	500 (R) + 100 (P)	116	Romney + Perendale	HD	Romney	5K
6_50KHD	500 (R) + 100 (P)	116	Romney + Perendale	HD	Romney	50K

^aImputation scenarios were from 5K to 50K (50K was a subset of the HD panel), 5K to HD and 50K to HD
^b2-Step imputation: from 5K to 50K using all genotyped animals as reference population (N = 17,000) and from 50K imputed to HD using 500 animals as the reference population
^cThe oldest animals in each scenario were used as reference population
^dThe youngest animals in each scenario were imputed

ISSN: 1297-9686