Fig. 2

Histograms and simulated distributions; library pairs. Histograms represent empirical distributions for minor allele (i.e. substitution) frequencies for 6 library pairs, which are derived by pooling minor allele frequencies of the two replicates for each of 6 “treatment” conditions (tissue by infection status) represented by the 12 libraries. Dashed curves represent distributions simulated from exponential-normal convolution models with parameter values estimated for each library pair (Table 1). Solid curves represent distributions simulated from the same models with parameters estimated on the library pair 1 and 2 (Table 1) appropriately “spiked” with low frequency substitutions (see insets) to account for their abundance in high coverage sequencing data. Note that for the pair 1 and 2, where coverage is lowest, dashed and solid curves are undistinguishable. The differences between the two curves are largest for pairs with highest coverage (see Table 1)