Table 4 Different quality measures of the estimated line B proportions derived with ADMIXTURE with various levels of pruning based on linkage disequilibrium (r2) in the broiler data
From: Estimation of dam line composition of 3-way crossbred animals using genomic information
Measure | r2 threshold for pruning | |||||
|---|---|---|---|---|---|---|
0.1 | 0.3 | 0.5 | 0.7 | 0.9 | No. | |
Number of SNPs | 3392 | 15,144 | 29,892 | 41,376 | 48,905 | 55,729 |
Accuracy | 0.839 | 0.914 | 0.927 | 0.927 | 0.925 | 0.918 |
Dispersion bias | 0.970 | 1.140 | 1.138 | 1.128 | 1.115 | 1.090 |
Maximum error | 0.094 | 0.073 | 0.066 | 0.064 | 0.068 | 0.070 |
RMSE | 0.024 | 0.018 | 0.017 | 0.017 | 0.017 | 0.018 |