Table 1.
Characteristics of different classes of variants used to simulate QTL
| Characteristic per class | Holstein-Friesian | Jersey | Total |
|---|---|---|---|
| Moderately low average MAF 1,2 | |||
| Segregating variants | 63 119 | 55 363 | 65 920 |
| Number of breed-specific variants | 10 557 | 2801 | 13 358 |
| Percentage of breed-specific variants | 16.0 | 4.2 | 20.3 |
| Average MAF1 of the 65 920 segregating variants (± standard deviation) | 0.130 ± 0.169 | 0.115 ± 0.168 | 0.122 ± 0.146 |
| Very low average MAF 1,3 | |||
| Segregating variants | 61 302 | 49 473 | 67 097 |
| Number of breed-specific variants | 17 624 | 5795 | 23 419 |
| Percentage of breed-specific variants | 26.3 | 8.6 | 34.9 |
| Average MAF1 of the 67 097 segregating variants (± standard deviation) | 0.082 ± 0.146 | 0.072 ± 0.142 | 0.077 ± 0.127 |
| Extremely low average MAF 1,4 | |||
| Segregating variants | 1804 | 1245 | 2142 |
| Number of breed-specific variants | 897 | 338 | 1235 |
| Percentage of breed-specific variants | 41.9 | 15.8 | 57.7 |
| Average MAF1 of the 2142 segregating variants (± standard deviation) | 0.017 ± 0.067 | 0.015 ± 0.066 | 0.016 ± 0.059 |
1MAF = minor allele frequency; 2annotated as synonymous mutations; 3annotated as missense mutations; 4annotated as premature stop codon mutations.