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

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

   Off0 Off1 Off2 Off4
Category n rsegregation rphased rsegregation rphased rsegregation rphased rsegregation rphased
Both parents 25 0.70 0.66 0.78 0.78 0.84 0.83 0.93 0.94
SireMGS 756 0.57 0.54 0.73 0.68 0.82 0.77 0.92 0.88
DamPGS 0 - - - - - - - -
Sire 15 0.50 0.48 0.69 0.68 0.80 0.78 0.93 0.87
Dam 0 - - - - - - - -
Other 9 0.13 0.13 0.61 0.61 0.77 0.77 0.91 0.91
Total1 805 0.57 0.54 0.73 0.68 0.82 0.77 0.92 0.88
runcorrected2 805 0.83 0.81 0.88 0.86 0.92 0.89 0.96 0.95
  1. 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.