Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle

Table 3 Average imputation accuracy (r) of 805 individuals with varying offspring information for different categories of individuals

Results from both AlphaImpute with phasing (phased) and only segregation analysis (segregation) are reported; average imputation accuracies were split into categories of the closest recent ancestor genotyped and calculated over 10 replications; ¹for AlphaImpute phased, the standard deviations for Total were 0.16, 0.13, 0.13, and 0.10 for scenarios Off0, Off1, Off2, and Off4, respectively; for segregation analyses, the standard deviations for Total were 0.12, 0.07, 0.07, and 0.05 for scenarios Off0, Off1, Off2, and Off4, respectively; ²mean of imputation accuracy calculated as the correlation between true genotypes and imputed genotype dosages, both uncorrected for the mean gene content.

ISSN: 1297-9686