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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

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

Adda Marker Number of markers
Reference panel Polymorphic in target panel Monomorphic in target panel Polymorphic in imputed target panel Falsely imputedb
0 All 625,538 607,560 17,978 593,239 1702
Rarec 140,584 122,606 17,978 108,379 1702
600 All 625,538 607,560 17,978 594,682 1831
Rarec 140,584 122,606 17,978 109,818 1831
1200 All 625,538 607,560 17,978 595,150 1856
Rarec 140,584 122,606 17,978 110,282 1856
1800 All 625,538 607,560 17,978 595,433 1880
Rarec 140,584 122,606 17,978 110,568 1880
2400 All 625,538 607,560 17,978 595,570 1886
Rarec 140,584 122,606 17,978 110,702 1886
  1. a Number of additional animals
  2. bNumber of markers that were imputed as polymorphic but were monomorphic in the base target (considering the true genotypes)
  3. cMAF < 2%