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

BMC Genomic Data

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

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.

ISSN: 2730-6844