Table 2.
Preselected SNPs based on different cutoff values for the FST scores and different simulation scenarios
| Panel density | QTL effects1 | Quantile | FST Score3 | Selected SNPs4 |
|---|---|---|---|---|
| 99.5 | 0.02 | 935 | ||
| Gamma5 | 99.0 | 0.01 | 1956 | |
| 97.5 | 0.004 | 4932 | ||
| 200 K | ||||
| 99.5 | 0.009 | 1076 | ||
| Predefined6 | 99.0 | 0.007 | 2171 | |
| 97.5 | 0.005 | 5620 | ||
| 99.5 | 0.015 | 2078 | ||
| Gamma | 99.0 | 0.009 | 3586 | |
| 97.5 | 0.004 | 10,178 | ||
| 400 K | ||||
| 99.5 | 0.009 | 2036 | ||
| Predefined | 99.0 | 0.007 | 4646 | |
| 97.5 | 0.004 | 10,651 | ||
1Distribution used for the simulation of the QTL effects, 2quantiles of the FST score distribution, 3cutoff point for the fixation index (FST), 4number of selected SNPs based on the FST score cutoff, 5Gamma distribution with shape parameter equal 0.4, and 6QTL effects pre-defined to explain at least 0.5% of genetic variance each