Table 2.

Relative effective sample size at imputed SNPs (ratio of the average ${\chi }^2$ association statistics attained at imputed versus typed SNPs) in simulated case–control studies at different effect sizes (OR >1)

Method	Odds Ratio (OR)
	1.0	1.2	1.5	1.7	2.0
	All SNPs
Beagle	0.999	0.892	0.872	0.870	0.868
ImpG-Summary	0.937	0.835	0.823	0.827	0.836
ImpG-SummaryLD	0.999	0.872	0.851	0.852	0.855
	Common SNPs (>5%)
Beagle	0.999	0.900	0.885	0.883	0.881
ImpG-Summary	0.956	0.850	0.841	0.845	0.855
ImpG-SummaryLD	0.999	0.882	0.867	0.868	0.872
	Low-frequency SNPs (1–5%)
Beagle	0.997	0.808	0.667	0.640	0.620
ImpG-Summary	0.881	0.685	0.539	0.512	0.491
ImpG-SummaryLD	0.997	0.768	0.597	0.565	0.542

Note: The column corresponding to OR = 1 shows the average ${\chi }^2$ association statistic under the null model of no association.