Table 5 Mean and standard deviation (SD) of concordance rate and allelic R ² calculated for different algorithms, panel densities and scenarios for both imputation to 50K and 777K SNP panels

Algorithm

Beagle

10

0.927

0.042

0.890

0.067

Fimpute

20

0.943

0.038

0.912

0.061

Panel

3K

6

0.864

0.011

0.787

0.016

6K

6

0.946

0.008

0.919

0.011

8K

6

0.952

0.008

0.927

0.011

15K

6

0.973

0.006

0.962

0.008

20K

6

0.953

0.008

0.929

0.011

Scenario

NE-P

5

0.943

0.041

0.913

0.065

NE-NP

10

0.935

0.041

0.901

0.066

NNE-P

5

0.943

0.042

0.912

0.067

NNE-NP

10

0.935

0.042

0.901

0.066

Algorithm

Beagle

8

0.895

0.040

0.826

0.066

Fimpute

16

0.921

0.035

0.866

0.059

Panel

3K¹

3

0.838

0.017

0.728

0.025

6K¹

3

0.898

0.016

0.829

0.025

8K¹

3

0.902

0.017

0.836

0.026

15K¹

3

0.918

0.017

0.863

0.027

20K¹

3

0.903

0.017

0.837

0.026

50K

3

0.930

0.016

0.882

0.025

90iK

3

0.952

0.010

0.919

0.016

90tK

3

0.955

0.009

0.925

0.014

Scenario

NE-P

8

0.9199

0.037

0.865

0.062

NE-NP

16

0.9082

0.039

0.846

0.065

Step

One-step

15

0.8064

0.884

0.674

0.147

Two-step

15

0.8920

0.032

0.819

0.053