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

		CR		Allelic R 2
	No.	Mean	SD	Mean	SD
		Imputation to the 50K SNP panel
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
		Imputation to the 777K SNP panel
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

¹Means and standard deviation for the two-step analysis.