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Table 7 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 777K SNP panel 1,2,3

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

Concordance rate Allelic R 2
Source Mean Scheffé test 4 Source Mean Scheffé test 4
Algorithm 5 (P-value < 0.0001) Algorithm 5 (P-value < 0.0001)
FImpute 1.291 a FImpute 1.203 a
Beagle 1.244 b Beagle 1.145 b
Panel 6 (P-value < 0.0001) Panel 6 (P-value < 0.0001)
90tK 1.351 a 90tK 1.286 a
90iK 1.343 b 90iK 1.275 b
50K 1.295 c 50K 1.210 c
15K 1.273 d 15K 1.181 d
20K 1.247 e 20K 1.146 e
8K 1.245 e 8K 1.144 e
6K 1.239 e 6K 1.135 e
3K 1.150 f 3K 1.013 f
Scenario 7 (P-value 0.0258) Scenario (P-value 0.0346)
NE-NP 1.269 a NE-NP 1.175 a
NE-P 1.267 b NE-P 1.172 b
Algorithm*panel (P-value =0.0052) Algorithm*panel (P-value =0.0107)
FImpute - 90tK 1.370 a FImpute - 90tK 1.309 a
FImpute - 90iK 1.364 a FImpute - 90iK 1.301 a
Beagle - 90tK 1.331 b Beagle - 90tK 1.262 b
FImpute - 50K 1.322 b Beagle - 90iK 1.249 b
Beagle - 90iK 1.322 b FImpute - 50K 1.244 b
FImpute - 15K 1.300 c FImpute - 15K 1.215 c
FImpute - 20K 1.271 d Beagle - 50K 1.176 d
FImpute - 8K 1.269 d FImpute - 20K 1.176 d
Beagle - 50K 1.269 d FImpute - 8K 1.174 d
FImpute - 6K 1.262 d FImpute - 6K 1.165 d
Beagle - 15K 1.245 e Beagle - 15K 1.146 e
Beagle - 20K 1.222 f Beagle - 20K 1.115 f
Beagle - 8K 1.221 f Beagle - 8K 1.114 f
Beagle - 6K 1.215 f Beagle - 6K 1.106 f
FImpute - 3K 1.169 g FImpute - 3K 1.039 g
Beagle - 3K 1.130 h Beagle - 3K 0.988 h
  1. 1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
  2. 2Interaction effects between Algorithm*Scenario and Panel*Scenario were not statistically significant (P > 0.05);
  3. 33K, 6K, 8K, 15K and 20K are low-density panels were imputed in two steps (firstly they were imputed to the 50K and then to the 777K SNP panel);
  4. 4Different letters within a group means that there is a statistical difference between two means (P < 0.05);
  5. 5Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
  6. 63K, 6K, 8K, 15K, 20K, 50K, 90iK and 90tK are low-density panels;
  7. 7Scenarios for imputation to the 777K SNP panel. (NE-P) - 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.