Table 4.

Overall computing run time in minutes for the different imputation scenarios ^1,2

Panel	FImpute				Beagle
	NE-P	NNE-P	NE-NP	NNE-NP	NE-NP	NNE-NP
	Imputation to the 50K SNP panel 3
3K	2	6	41	39	2280	2131
6K	3	7	46	45	828	772
8K	3	7	45	45	808	656
15K	3	9	48	48	328	317
20K	3	7	37	42	708	622
	Imputation to the 777K SNP panel 4,5
3K	16 (17,24)	-	4 (5,8)	-	64 (224,41)	-
6K	17 (23,24)	-	4 (19,21)	-	49 (238,33)	-
8K	17 (23,24)	-	3 (20,23)	-	45 (177,34)	-
15K	15 (24,23)	-	8 (20,23)	-	40 (127,42)	-
20K	17 (23,23)	-	9 (20,23)	-	44 (161,42)	-
50K	3	-	11	-	29	-
90iK	17	-	11	-	25	-
90tK	17	-	10	-	33	-

¹Run time based on 10 parallel jobs with computer with 4*6-core processors (Intel Xeon X5690 @ 3.47GHz) and 128 Gigabytes of memory in OS x86-64 GNU/Linux;

²Scenarios for imputation. (NE-P) - using Nellore genotypes in the reference population and considering pedigree information; (NNE-P) - not using Nellore genotypes in the reference population and considering pedigree information; (NE-NP) - using Nellore genotypes in the reference population and not using pedigree information; (NNE-NP) - not using Nellore genotypes in the reference population and not using pedigree information;

³2,735 or 2,647 (not using Nellore genotypes) animals in the reference population and 963 animals in the imputation population;

⁴Values outside the brackets refer to the one-step imputation. The reference and imputation population were formed by 175 and 43 animals, respectively;

⁵Values inside the brackets refer to the two-step imputation. The reference population were formed by 3,567 in the imputation from low density panel to the 50K SNP panel and 175 animals in the imputation from the 50K SNP panel to the 777K SNP panel. The imputation population was formed by 43 animals.