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Table 6 Average allelic R2 measure from Beagle and true imputation reliability on GGA1 for different MAF classes and different reference sizes (48K to 60K scenario)

From: Accuracy of imputation using the most common sires as reference population in layer chickens

 

Ref22

Ref62

MAF1 class

Reliabilitya

Allelic R2

Reliability

Allelic R2

0.008–0.1

0.59

0.64

0.68

0.75

0.1–0.2

0.73

0.77

0.79

0.85

0.2–0.3

0.78

0.80

0.83

0.88

0.3–0.4

0.81

0.82

0.85

0.90

0.4–0.5

0.79

0.81

0.83

0.87

  1. 1 Minor allele frequency
  2. aReliability is the square of imputation accuracy per SNP across individuals (SNP-specific imputation accuracy), i.e. the imputation accuracy per SNP was squared and were then summed across individuals. Note that the values in this table are average across the three generations (G0, G1 and G2)
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BMC Genomic Data

ISSN: 2730-6844

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