Summary of genes affected by convergent evolution due to indels.

“Parsimony informative” states whether the variant considered is parsimony informative (Yes) or not (No). “Parsimony score” gives the minimum number of events required to explain the evolution of the variant on the phylogeny. “# SNPs in gene” gives the number of SNPs found in the gene considered. “Position in gene” describes the localization of variants in coding regions by the gene coordinates. The essential category can be either essential (i.e., the gene is required for growth in vitro) or dispensable (i.e., the gene is not required for growth in vitro). “Antibiotic resistance” describes whether the gene has been found to confer antibiotic resistance upon substitutions (“Res”, according to S2 Table) or not (“NRes”). (XLSX)