To further measure the precision of the ancestry estimation of individual subjects in admixed populations, we examined the 90% confidence intervals. For each individual the 90% Bayesian confidence interval was measured (STRUCTURE output). For each set of AIMs, the average size of this confidence interval was then calculated (Table 4). Comparison of these results shows the decrease in individual confidence intervals based on the number of markers and the dependency on the admixed population being analyzed. These confidence limits show that in studies of AFA, smaller sets can still provide good precision in individual admixture measurement. However, for MAM/MXN relatively larger numbers of AIMs are required. The confidence limits are smaller when In2 marker sets optimized for the particular admixed population are used. However, the 96 In 4 and 128 In4 set appear to perform very well in each of the admixed groups.
