A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

Table 1 Accuracy of imputation for the pig dataset

		Pig99		Pig95		Pig90		Pig85		Unmapped
Category¹	Count²	AI³	I2⁴	AI³	I2⁴	AI³	I2⁴	AI³	I2⁴	AI³
BothParents	51	0.98	0.77	0.99	0.92	1.00	0.96	1.00	0.96	0.83
SireMGS	62	0.93	0.80	0.98	0.92	0.99	0.94	0.99	0.96	0.78
DamPGS	47	0.96	0.79	0.98	0.92	0.99	0.95	0.99	0.96	0.82
Sire	45	0.89	0.78	0.97	0.92	0.99	0.95	0.99	0.97	0.78
Dam	13	0.90	0.76	0.96	0.89	0.98	0.93	0.98	0.95	0.73
Other	291	0.86	0.79	0.94	0.91	0.97	0.95	0.97	0.96	0.76

¹Animals in the testing set were divided into six categories depending on their pattern of relationship to their most recent densely genotyped ancestors; the categories were: both parents genotyped (BothParents); sire and maternal grandsire (SireMGS); dam and paternal grandsire (DamPGS); sire only (Sire); dam only (Dam); and other relatives (Other); ²Count refers to the number of individuals in each category; ³AI = AlphaImpute; I2⁴=IMPUTE2.

ISSN: 1297-9686