Fig. 3

Rifampicin resistance-associated mutations detected by RM-seq. Three independent selection experiments of ~ 10,000 resistant colonies were assessed by RM-seq of the rpoB gene RRDR region. The histograms (upper) represent the normalised mutation counts identified along the sequenced region of the RRDR for the three different selection experiments, with bar colour representing the types of mutation (red for deletions, green for insertions and blue for substitutions). The range of mutations affecting each residue is depicted in the associated heat map (lower panel). The intensity of the blue represents allele frequencies for each selection experiment. Mutations observed from consensus reads reconstructed with at least 10 reads and with a relative frequency greater than 6 × 10⁻⁵ or identified from all three independent selection experiments are represented. Resistance mutations that were confirmed by genetic reconstruction are indicated in red (Additional file 1: Table S3). Mutations and positions previously associated with rifampicin resistance are indicated with a star