Table 1.

Numbers of pigs sequenced and imputed

Line	Individuals sequenced	Individuals sequenced by coverage				Individuals used in the analyses
		1x	2x	5x	15–30x	Pedigree	LD	HD	Imputed
A	1856	1044	649	73	90	122,753	39,485	66,763	104,661
B	1366	685	545	44	92	88,964	39,110	38,763	76,230
C	1491	628	728	54	81	84,420	35,343	34,358	66,608
D	731	362	311	16	42	79,981	16,650	54,297	60,474
E	760	394	274	27	65	50,797	22,768	20,685	41,573
F	381	193	137	16	35	35,309	11,747	17,758	29,330
G	445	217	176	15	37	21,129	11,472	6661	17,224

Pedigree number of individuals included in the pedigree used for imputation, LD number of individuals genotyped with the low-density marker array, HD number of individuals genotyped with high-density marker arrays, Imputed number of individuals with imputed genotypes that remain after filtering out individuals with low predicted imputation accuracy