Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle

Table 4 Average percentage of correct, incorrect or not imputed genotypes per individual for each scenario and for different categories of individuals

Scenario	Imputed	Both parents	SireMGS	DamPGS	Sire	Dam	Other	Total
Segregation
Real	Correct	52.9	20.3	33.6	16.8	45.9	11.9	14.3
	Incorrect	0.0	0.2	0.4	0.2	0.7	0.2	0.2
	Not imputed	47.0	79.4	66.0	82.9	53.4	87.8	85.5
SireMGS	Correct	52.8	17.9	-	9.0	-	7.2	18.7
	Incorrect	0.0	0.1	-	0.1	-	0.2	0.1
	Not imputed	47.1	81.9	-	90.8	-	92.6	81.2
Off0	Correct	51.1	14.4	-	6.6	-	6.5	15.3
	Incorrect	0.0	0.1	-	0.1	-	0.2	0.1
	Not imputed	48.8	85.4	-	93.2	-	93.2	84.6
Off1	Correct	57.9	30.3	-	19.4	-	7.2	30.8
	Incorrect	0.2	1.15	-	1.3	-	0.1	1.1
	Not imputed	41.7	68.4	-	79.2	-	92.6	68.1
Off2	Correct	61.6	39.3	-	31.0	-	11.9	39.6
	Incorrect	0.2	0.9	-	1.4	-	0.2	0.8
	Not imputed	38.1	59.7	-	67.5	-	87.9	59.6
Off4	Correct	67.5	50.7	-	46.3	-	35.7	51.0
	Incorrect	0.1	0.3	-	0.2	-	0.2	0.3
	Not imputed	32.4	48.9	-	53.4	-	64.0	48.7
Phased
Off0	Correct	40.8	12.4	-	4.9	-	4.7	13.1
	Incorrect	15.3	4.3	-	1.6	-	1.7	4.6
	Not imputed	43.8	83.2	-	93.3	-	93.5	82.3
Off1	Correct	71.8	43.4	-	22.1	-	7.0	43.5
	Incorrect	4.0	6.2	-	3.3	-	0.1	6.0
	Not imputed	24.1	50.3	-	74.6	-	92.8	50.5
Off2	Correct	73.4	60.1	-	37.1	-	11.8	59.6
	Incorrect	1.5	5.2	-	4.2	-	0.2	5.0
	Not imputed	25.0	34.6	-	58.7	-	87.9	35.4
Off4	Correct	87.4	78.4	-	61.7	-	35.9	78.0
	Incorrect	0.5	2.7	-	4.1	-	0.2	2.6
	Not imputed	12.1	18.8	-	34.2	-	63.8	19.4

For the offspring scenarios, results from both AlphaImpute with phasing (phased) and only segregation analysis (segregation) are given; average percentages were split into categories of the closest recent ancestor genotyped and calculated over 10 replications.

ISSN: 1297-9686