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)
| 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 |