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Table 4 Average percentage of correct, incorrect or not imputed genotypes per individual for each scenario and 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

Scenario Imputed Both parents SireMGS DamPGS Sire Dam Other Total
Segregation        
Real Correct 52.9 20.3 33.6 16.8 45.9 11.9 14.3
  Incorrect 0.0 0.2 0.4 0.2 0.7 0.2 0.2
  Not imputed 47.0 79.4 66.0 82.9 53.4 87.8 85.5
SireMGS Correct 52.8 17.9 - 9.0 - 7.2 18.7
  Incorrect 0.0 0.1 - 0.1 - 0.2 0.1
  Not imputed 47.1 81.9 - 90.8 - 92.6 81.2
Off0 Correct 51.1 14.4 - 6.6 - 6.5 15.3
  Incorrect 0.0 0.1 - 0.1 - 0.2 0.1
  Not imputed 48.8 85.4 - 93.2 - 93.2 84.6
Off1 Correct 57.9 30.3 - 19.4 - 7.2 30.8
  Incorrect 0.2 1.15 - 1.3 - 0.1 1.1
  Not imputed 41.7 68.4 - 79.2 - 92.6 68.1
Off2 Correct 61.6 39.3 - 31.0 - 11.9 39.6
  Incorrect 0.2 0.9 - 1.4 - 0.2 0.8
  Not imputed 38.1 59.7 - 67.5 - 87.9 59.6
Off4 Correct 67.5 50.7 - 46.3 - 35.7 51.0
  Incorrect 0.1 0.3 - 0.2 - 0.2 0.3
  Not imputed 32.4 48.9 - 53.4 - 64.0 48.7
Phased        
Off0 Correct 40.8 12.4 - 4.9 - 4.7 13.1
  Incorrect 15.3 4.3 - 1.6 - 1.7 4.6
  Not imputed 43.8 83.2 - 93.3 - 93.5 82.3
Off1 Correct 71.8 43.4 - 22.1 - 7.0 43.5
  Incorrect 4.0 6.2 - 3.3 - 0.1 6.0
  Not imputed 24.1 50.3 - 74.6 - 92.8 50.5
Off2 Correct 73.4 60.1 - 37.1 - 11.8 59.6
  Incorrect 1.5 5.2 - 4.2 - 0.2 5.0
  Not imputed 25.0 34.6 - 58.7 - 87.9 35.4
Off4 Correct 87.4 78.4 - 61.7 - 35.9 78.0
  Incorrect 0.5 2.7 - 4.1 - 0.2 2.6
  Not imputed 12.1 18.8 - 34.2 - 63.8 19.4
  1. For the offspring scenarios, results from both AlphaImpute with phasing (phased) and only segregation analysis (segregation) are given; average percentages were split into categories of the closest recent ancestor genotyped and calculated over 10 replications.