Fig. 4
Homoplastic (grew bars) and non-homoplastic (white bars) variants (SNPs versus InDels, intragenic versus intergenic, non-synonymous versus synonymous) fixed across all branches of the phylogenetic inference including genomes of Salmonella enterica subsp. enterica serovars Enteritidis (n = 33), Pullorum (n = 5), Gallinarum (n = 8) and Dublin (n = 13). The variant annotation was performed with SnpEff against reference genome S. Enteritidis (strain P125109, accession NC_011294.1). The fixed non-homoplastic variants are defined by common genotypes across the considered group of genomes, as well as different genotypes in all the others compared genomes. The fixed homoplastic variants are defined by common genotypes across the considered group of genomes and genomes of independent phylogenetic clades, as well as different genotypes in genomes of the compared child-branches. The term ‘reference genotype’ refers to fixed variants presenting genotype of the reference genome. This analysis was performed with the script ‘phyloFixedVar’ (i.e. dependently of the phylogenetic inference). Statistical differences (*: p < 1.0×10−6; **: p < 1.0×10−7; ***: p < 1.0×10−8; ****: p < 1.0×10−9; *****: p < 1.0×10−10) are calculated with Wilcoxon signed rank tests. The vertical bars represent the standard deviation