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

Table 4 Number of polymorphic and monomorphic markers in n = 1000 reference and n = 500 target animals when different numbers of additional animals were included for phase inference in the 500 target animals

Add^a	Marker	Number of markers
Add^a	Marker	Reference panel	Polymorphic in target panel	Monomorphic in target panel	Polymorphic in imputed target panel	Falsely imputed^b
0	All	625,538	607,560	17,978	593,239	1702
0	Rare^c	140,584	122,606	17,978	108,379	1702
600	All	625,538	607,560	17,978	594,682	1831
600	Rare^c	140,584	122,606	17,978	109,818	1831
1200	All	625,538	607,560	17,978	595,150	1856
1200	Rare^c	140,584	122,606	17,978	110,282	1856
1800	All	625,538	607,560	17,978	595,433	1880
1800	Rare^c	140,584	122,606	17,978	110,568	1880
2400	All	625,538	607,560	17,978	595,570	1886
2400	Rare^c	140,584	122,606	17,978	110,702	1886

^a Number of additional animals
^bNumber of markers that were imputed as polymorphic but were monomorphic in the base target (considering the true genotypes)
^cMAF < 2%

ISSN: 1471-2164