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Table 3 Imputation accuracy (R2dose) in 500 target samples when additional animals were used for haplotype inference

From: Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

 

Number of additional samples used for the phasing of 500 target base animals

0

600

1200

1800

2400

Rare (MAF < 2%)

0.748

0.760

0.765

0.767

0.768

Low-frequency (MAF < 5%)

0.804

0.815

0.819

0.820

0.821

Common (MAF > 5%)

0.948

0.952

0.953

0.954

0.954

Global

0.903

0.910

0.912

0.913

0.913