Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost

Table 1 Description of SNP panels for chromosome 1

SNP panel code	SNP panel design¹	Number of SNP on chromosome 1	Equivalent density across the genome	Average spacing (kb) ± SD	Cost per genotyped animal
H	High density	5 936	60 000	77. 30 ± 65.22	$120
L6k	89.9 % SNP masked	600	6 065	458. 76 ± 187.79	$48
L3k	95.0 % SNP masked	299	3 022	913. 96 ± 402.26	$35
L384	99.4 % SNP masked	37	384	7359.28 ± 3403.54	$20

¹A reduced SNP panel with m SNP was designed as selecting the highest MAF SNP in each of m non-overlapping sliding windows where m has a value of 600, 299 and 37 for reduced panel L6k, L3k and L384, respectively; these sliding windows were evenly spaced windows according to their map distances.

ISSN: 1297-9686