Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

Table 2 Number of polymorphic and monomorphic markers in reference, target and imputed data

Ref^a	Marker	Number of markers
Ref^a	Marker	Polymorphic in reference panel	Polymorphic in target panel	Monomorphic in target panel	Polymorphic in imputed data	Falsely imputed^b
250	All	597,095	595,609	1486	586,701	526
250	Rare^c	114,516	113,030	1486	104,222	526
500	All	613,649	610,987	2661	601,082	711
500	Rare^c	129,107	126,446	2661	116,619	711
1000	All	626,122	621,698	4424	611,284	860
1000	Rare^c	140,931	136,507	4424	126,155	860
2000	All	636,201	629,025	7176	618,660	990
2000	Rare^c	150,407	143,231	7176	132,931	990

^aReference panel size
^bNumber of markers that were imputed as polymorphic but were monomorphic in the target animals (considering the true genotypes)
^cMAF < 2%

ISSN: 1471-2164