Fig. 5

Comparison of K or X and pairwise LD in real data. Four panels designed from real dataset by variant pruning with threshold 0.2, 0.4, 0.6 and 0.8 are tested in pairwise LD and summary statistic K and X. In each panel, there are 2067, 3157, 4278 and 5754 variants, respectively. a is the boxplot excluding outliers of \(r^{2}\) values for each panel. With the threshold increasing (x-axis denotes the groups), the boxplot lifts but major parts remain under 0.2. b is the power of pairwise LD by GDA, K, and X in multiple trials (10 trials for GDA, 1000 trials for K or X) for 100 random markers from each panel. On each new trial, the markers were re-selected. Y-axis shows the proportion of significant p values on each panel. The number of trials for GDA is small due to the time-consuming of this software. The power in this method might not be accurate. Average proportions for significant p values in method GDA is: 0.047 (0.2 group); 0.041 (0.4 group), 0.054 (0.6 group), 0.040 (0.8 group)