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Table 1 Measures of imputation success for single- and mixed-density data by age group

From: Genomic evaluations with many more genotypes

Markers used   50 K Mixed Mixed 500 K
Number of 500 K genotypes   0 1,406 3,798 33,414
  Age1:     
Missing before imputation (%) all 1 86 80 1
Missing after imputation (%) all 0.04 6.4 3.3 0.05
Genotype error rate (%) young 0.03 1.3 0.9 0.03
  old 0.04 3.4 1.7 0.04
Incorrect genotypes (%) young 0.06 2.6 1.7 0.06
  old 0.08 7.3 3.4 0.08
Incorrect linkage phase (%) young 0.3 1.9 1.4 0.1
  old 0.4 5.4 2.5 0.2
Incorrect paternity (%) young 2.0 4.9 5.0 2.5
  old 4.3 7.6 6.2 4.2
Correlation2 (estimated, true genotypes) all 0.99 0.84 0.93 0.99
Reliability of linear breeding values (%) young 82.6 83.4 83.7 84.1
Reliability of nonlinear breeding values (%) young 84.4 85.3 85.6 86.0
Reliability gain (nonlinear), 500 K - 50 K (%) young 0.0 0.9 1.2 1.6
  1. 1old are animals with phenotypes or progeny; young are animals without
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