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Table 8 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 to the 777K SNP panel by one or two steps 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
Step 4 (P-value < 0.0001) Step 4 (P-value < 0.0001)
Two-step 1.231 a Two-step 1.125 a
One-step 1.110 b One-step 0.997 b
Algorithm 5 (P-value < 0.0001) Algorithm 4 (P-valeu 0.0001)
FImpute 1.202 a FImpute 1.080 a
Beagle 1.140 b Beagle 0.997 b
Panel 6 (P-value < 0.0001) Panel 6 (P-value < 0.0001)
15K 1.236 a 15K 1.130 a
20K 1.229 b 20K 1.120 a
8K 1.180 c 8K 1.052 b
6K 1.167 d 6K 1.034 c
3K 1.042 e 3K 0.855 d
Scenario 7 (P-value 0.7638) Scenario 7 (P-value 0.9983)
NE-NP 1.171 a NE-NP 1.038 a
NE-P 1.170 a NE-P 1.038 a
Step*Algorithm (P-value < 0.0001) Step*Algorithm (P-value < 0.0001)
Two-step - FImpute 1.254 a Two-step - FImpute 1.154 a
Two-step - Beagle 1.208 b Two-step - Beagle 1.095 b
One-step - FImpute 1.149 c One-step - FImpute 1.006 c
One-step - Beagle 1.072 d One-step - Beagle 0.898 d
Step*Panel (P-value < 0.0001) Step*Panel (P-value < 0.0001)
Two-step - 15K 1.274 a Two-step - 15K 1.183 a
Two-step - 20K 1.247 b Two-step - 20K 1.147 b
Two-step - 8K 1.246 b Two-step - 8K 1.145 b
Two-step - 6K 1.239 b Two-step - 6K 1.136 b
One-step - 20K 1.210 c One-step - 20K 1.094 c
One-step - 15K 1.198 c One-step - 15K 1.078 c
Two-step - 3K 1.149 d Two-step - 3K 1.013 d
One-step - 8K 1.114 e One-step - 8K 0.960 e
One-step - 6K 1.094 f One-step - 6K 0.932 e
One-step - 3K 0.936 g One-step - 3K 0.696 f
  1. 1Concordance rate and allelic R2 were arcsine square root transformed for the analyses;
  2. 2Interaction effects between step*scenario, algorithm*panel, 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. 4One-step is the imputation from the low-density panels to the 777K SNP panel and two-step is the imputation from low-density panels to 50K SNP panel and after the imputation from 50K SNP panel to 777K SNP panel;
  5. 5Algorithm used was either FImpute v.2.2 [11] or Beagle v.3.3 [8];
  6. 63K, 6K, 8K, 15K, and 20K 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.