Additional file 6: of First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts

Phylogenetically relevant single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels) fixed at phylogenetic branches where genomes of Salmonella enterica subsp. enterica serovars Enteritidis (n = 33), Pullorum (n = 5), Gallinarum (n = 8) and Dublin (n = 13) diverged. The variant calling analysis was performed with the ‘VARCall’ workflow (i.e. 12,929 SNPs and 1157 small InDels). 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-leaves. The variants were annotated with SnpEff against reference genome S. Enteritidis (strain P125109, accession NC_011294.1). (XLSX 13 kb)