Figure 6

Observed type I error rate when there is misclassification error between SRE and admixture. We observed significant type I error inflation in figure 6a that is due to the possibility for misclassification error described in figure 5a. Once we the ambiguity is removed (figure 5b) and there is no possible misclassification errors, we see that observed type error rate is maintained at the preset significance level. The distribution of allele frequencies in the 3 ancestral populations appears to also affect the degree of confounding that occurs, such that the type I error inflation due to misclassification errors is worst for some cases than it is for others. For example, when we changed the allele frequency of marker G₂ from (0.2, 0.4, 0.6) to (0.4, 0.2, 0.6) to make it independent but identically distributed with G₁ then the observed type I error rate dropped from 0.165 to 0.07. We repeated the same experiment by keeping the frequency of G₁ fixed and changing the frequency of G₂ to (0.1, 0.3, 0.5). The observed type I error is now 0.18, and again by changing the order of the first 2 components of the allele frequency vector, this type I error is reduced to 0.065. The type I error associated with the scenario described in figure 5b remain around the preset threshold of 0.05 independently of the choice of allele frequencies in the 3 ancestral populations.