FIG. 3.

(a) LRT1: Comparing a simple model that assumes uniform relative abundances (the null hypothesis) to eALPS (the alternative hypothesis), using an LRT on every SNP separately. Permutations were performed to obtain p-values that are visualized using a QQ-plot. It is evident that the p-values are systematically smaller than the expected uniform distribution under the null, suggesting that the null hypothesis can be rejected. (b) LRT2: Comparing eALPS (the null hypothesis) to a model that allows relative abundances to vary across positions. The green points are p-values for all positions, and the blue points are the p-values after discarding putative genotype errors according to an error probability of 0.05. In both plots, the x-axis is the – log of p-values drawn from the uniform distribution (uniform quantile), and the y-axis is the – log of the p-values. LRT, likelihood ratio test.