Investigation into the Effects of Number of SNPs and Number of Reference Individuals on Imputation Accuracy

Abstract

Imputation is used in Australia’s national beef genetic evaluation, BREEDPLAN, to resolve missing genomic information in the combined panels of genomic data and clarify relationships through building a genomic relationship matrix (GRM). The accuracy of imputation is dependent on many factors such as the size of reference population and the density of markers. Here we demonstrated an improvement in imputation accuracy of Angus genotypes by increasing the numbers of individuals and the density of markers in the reference population. The results show a considerable increase in imputation accuracy by increasing density of markers up to 15k SNPs.