Fig. 3

Power and significance level (proportion of p values < 0.05) for different levels of linkage. X-axis denotes the number of markers in one panel; Y-axis denotes the proportion of cases when p values < 0.05 out of 1000 cases. For the completely unlinked panels, this proportion means significance level (Type I error) in null hypothesis; for other panels with linkages, this proportion means power (1- type II error) of these two methods. a–c are figures of K and d–f are figures of X. a, d are panels with all linked markers are SNPs; b, e are panels with all linked markers on STRs; c, f are panels with equal number of linked SNPs and STRs. In condition, power increases with panel size extends; linkage on SNPs contributes more power than STRs; and K shows more power than X. For SNP-biased (linkage on SNPs) panels, dependency can be detected when linkage is quarter-linked or more; but for STR-biased panels, only three-quarter-linked and almost -linked panels can be tested as dependent panels. In unbiased panels, half-quarter-linkage are also hardly to be detected