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Table 2 Number of markers in each scenario and their mean minor allele frequency in Dutch Holsteins (DH), New Zealand Holsteins (NZH) and New Zealand Jerseys (NZJ)

From: Utility of whole-genome sequence data for across-breed genomic prediction

Scenario

Number of SNPs

Mean MAF

DH

NZH

NZJ

Scenarios with unselected SNPs

Full_seq

14,341,737

0.18

0.17

0.15

HD

583,078

0.27

0.28

0.24

50k

48,912

0.25

0.26

0.21

Scenarios with unselected + selected SNPs

HD_TOP

583,194

0.27

0.28

0.24

50k_TOP

49,045

0.25

0.25

0.21

Scenarios with only selected SNPs

Pval5

59,828

0.25

0.23

0.17

Pval7

23,125

0.24

0.23

0.17

COJO3

1570

0.18

0.17

0.13

COJO8

360

0.20

0.21

0.13

Top_markers

133

0.23

0.24

0.16