Description of incompatible SNPs.

The column “Effect” gives the effect of the SNPs on the resulting protein, i.e., non-synonymous (NS) or synonymous (S). “Parsimony score” gives the number of independent events required to explain the evolution of the variant on the phylogeny. “Number of samples” describes the number of samples where the variant is detected. “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”). “Comment” describes the genomic distance of intergenic variants from the neighboring genes. Intergenic variants are split in two rows, where the first row describes the gene before the variant, and the second row describes the gene after the variant, in genomic coordinates.
(XLSX)