Population differentiation between samples.

<p>A.) Pairwise F_ST of polymorphic sites. Each patient sample was treated as a population and F_ST was calculated individually for each polymorphic site in a population. Calculations were performed on all polymorphic sites covered by at least 10 reads per sample for which the minor allele was supported by a minimum of 6 reads across all samples from the population (<i>see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005257#sec013" target="_blank">Methods</a></i>). Dots show the highest observed F_ST value for each single nucleotide polymorphism (SNP) across the H37Rv genome. Red color coding indicates allele frequencies changed significantly across the sampling interval (based on a Fisher’s exact test; <i>q</i>-value < 0.01). Genes implicated in drug resistance are outlined in black. Outliers of the F_ST distribution are likely to be under positive selection, or linked to a mutation under positive selection. B.) Allele frequencies over the course of treatment for SNPs with significant changes in allele frequency (red dots in A).