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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

From: Accuracy of genome-wide imputation in Braford and Hereford beef cattle

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
  1. 1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
  2. 2Interactions between Algorithm*Scenario and Panel*Scenario were not statistically significant (P > 0.05);
  3. 3Different letters within a group means that there is a statistical difference between two means (P < 0.05);
  4. 4Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
  5. 53K, 6K, 8K, 15K and 20K are low-density panels;
  6. 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.