Table 2 Mutations of Salmonella enterica subsp. enterica serovars (n = 440) associated with animal sources (i.e. avian bovine, swine and fish) by microbial GWAS including or excluding variants from recombination events. The accessory genes and coregenome variants (i.e. SNPs and InDels) were annotated with Prokka (1.12) and SNPeff (4.1 g), respectively. After potential exclusion of variants from recombination events based on iVARCall2 and ClonalFrameML, the workflow ‘microbial-GWAS’ corrects the population structure based on Linear Mixed Model (LMM), then perform associations with Wald tests implemented in GEMMA. The associated mutations (i.e. Wald tests) refer to polygenicity with regard to Quantile-Quantile (QQ) plots from microbial GWAS (i.e. p < 1 × 10^− 3 and p < 1 × 10^− 2, with or without recombination events) and present high (i.e. > 5%) and low (i.e. < 5‰) frequencies of presence (i.e. genes and alternative variants) in the studied and compared genomes, respectively

From: Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale