Localization and description of the effect of parsimony informative indels.

The column “Parsimony score” gives the minimum number of events required to explain the evolution of the variant on the phylogeny. Parsimony scores above 1 indicate incompatible variants. “Number of samples” describes the number of samples affected by the variant. “Effect” is either “IS6110 insertion”, “homopolymer” for an indel in a region with at least 3 repeated nucleotides, “in-frame” if the indel preserves the frame of the gene, “long deletion” for deletions longer than 50bp, or “other” for the remaining indels. “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 whether a gene is partially or completely deleted in the case of long deletions or 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. Of note, four of the 10 incompatible short indels are found in homopolymer regions (positions 1,333,640bp, 4,140,029bp, 4,324,110bp and 4,359,787bp). In addition, four intergenic short indels that are incompatible likely stem from the same event, potentially involving a DNA translocation (positions 2,436,569bp, 2,436,573bp, 2,436,584bp and 2,436,585bp). The two remaining incompatible short indels constitute (i) an in-frame short deletion in a PE gene (position 1,212,205bp) and (ii) a 1bp insertion leading to a frameshift (and a modified protein sequence that is 28 amino acids longer), in a gene encoding a nitronate monooxygenase (position 3,082,251bp).
(XLSX)