Table 2.
Comparison of models used to estimate genomic inbreeding coefficients with different numbers of HBD classes (from 1 to 4)
| Panel density | Na | Number of fitted HBD classes | Mean FG | Correlation with FbG-8192 | Median of estimated R k rates per HBD class | |||
|---|---|---|---|---|---|---|---|---|
| 1st HBD class | 2nd HBD class | 3rd HBD class | 4th HBD class | |||||
| LD | 634 | 1 | 0.058 | 0.982 | 15 | |||
| LD | 0 | 2 | 0.061 | 0.998 | 11 | 106 | ||
| LD | 0 | 3 | 0.061 | 0.999 | 11 | 104 | 162 | |
| LD | 0 | 4 | 0.061 | 0.999 | 10 | 42 | 150 | 175 |
| 50 K | 289 | 1 | 0.083 | 0.983 | 41 | |||
| 50 K | 345 | 2 | 0.094 | 0.999 | 15 | 198 | ||
| 50 K | 0 | 3 | 0.094 | 1.000 | 14 | 173 | 238 | |
| 50 K | 0 | 4 | 0.094 | 1.000 | 11 | 64 | 240 | 243 |
| HD | 0 | 1 | 0.297 | 0.999 | 1214 | |||
| HD | 0 | 2 | 0.302 | 1.000 | 60 | 1679 | ||
| HD | 629 | 3 | 0.303 | 1.000 | 22 | 392 | 1887 | |
| HD | 5 | 4 | 0.303 | 1.000 | 19 | 342 | 1823 | 1914 |
| WGS | 0 | 1 | 0.354 | 1.000 | 3740 | |||
| WGS | 0 | 2 | 0.359 | 1.000 | 577 | 8158 | ||
| WGS | 27 | 3 | 0.359 | 1.000 | 55 | 1009 | 8192 | |
| WGS | 23 | 4 | 0.359 | 1.000 | 21 | 206 | 1104 | 8192 |
The R k rates of each HBD class were estimated for each individual and for each SNP density (LD, 50 K, HD panels or whole-genome sequence data). The table reports which models are selected as best based on the BIC criterion, the average FG and its correlation with a reference FG obtained with a model using 13 HBD classes
aN = number of individuals with the corresponding model selected as best based on the BIC
bThe reference inbreeding coefficient FG-8192 is obtained with a Mix14R model and the same SNP density