Table 6.
Analysis of variance performed on the average concordance rate and allelic R 2 of the animals in the imputation population from each scenario for imputation from low density panels to the 50K SNP panel 1,2
| Concordance rate | Allelic R 2 | ||||
|---|---|---|---|---|---|
| Source | Mean | Scheffé test 3 | Source | Mean | Scheffé test 3 |
| Algorithm 4 (P-value < 0.0001) | Algorithm 4 (P-value?<?0.0001) | ||||
| FImpute | 1.340 | a | FImpute | 1.283 | a |
| Beagle | 1.306 | b | Beagle | 1.244 | b |
| Panel 5 (P-value < 0.0001) | Panel 5 (P-value?<?0.0001) | ||||
| 15K | 1.402 | a | 15K | 1.368 | a |
| 20K | 1.347 | b | 20K | 1.295 | b |
| 8K | 1.345 | c | 8K | 1.292 | c |
| 6K | 1.332 | d | 6K | 1.276 | d |
| 3K | 1.189 | e | 3K | 1.085 | e |
| Scenario 6 (P-value 0.0147) | Scenario 6 (P-value 0.0277) | ||||
| NE-P | 1.323 | a | NE-P | 1.264 | a |
| NNE-P | 1.323 | a | NE-NP | 1.263 | a |
| NE-NP | 1.323 | a | NNE-P | 1.264 | a |
| NNE-NP | 1.322 | a | NNE-NP | 1.262 | a |
| Algorithm*Panel (P-value < 0.0001) | Algorithm*Panel (P-value 0.0265) | ||||
| FImpute - 15K | 1.420 | a | FImpute -15K | 1.388 | a |
| Beagle - 15K | 1.384 | b | Beagle - 15K | 1.347 | b |
| FImpute - 20K | 1.365 | c | FImpute - 20K | 1.316 | c |
| FImpute - 8K | 1.362 | d | FImpute - 8K | 1.312 | d |
| FImpute - 6K | 1.349 | e | FImpute - 6K | 1.295 | e |
| Beagle - 20K | 1.330 | f | Beagle - 20K | 1.275 | f |
| Beagle - 8K | 1.328 | f | Beagle - 8K | 1.272 | f |
| Beagle - 6K | 1.316 | g | Beagle - 6K | 1.257 | g |
| FImpute - 3K | 1.204 | h | FImpute - 3K | 1.104 | h |
| Beagle - 3K | 1.174 | i | Beagle - 3K | 1.067 | i |
1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
2Interactions between Algorithm*Scenario and Panel*Scenario were not statistically significant (P?>?0.05);
3Different letters within a group means that there is a statistical difference between two means (P?<?0.05);
4Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
53K, 6K, 8K, 15K and 20K are low-density panels;
6Scenarios for imputation to the 50K SNP panel. (NE-P) - using Nellore genotypes in the reference population and considering pedigree information; (NNE-P) - not using Nellore genotypes in the reference population and considering pedigree information; (NE-NP) - using Nellore genotypes in the reference population and not using pedigree information; (NNE-NP) - not using Nellore genotypes in the reference population and not using pedigree information.