Table 3 Mutations before and after microbial GWAS aiming to associate animal sources (i.e. avian bovine, swine and fish) with mutations from accessory (i.e. genes) and coregenome (i.e. SNPs and InDels) of Salmonella enterica subsp. enterica serovars (n = 440). The accessory genes and coregenome variants (i.e. SNPs and InDels) were annotated with Prokka (1.12) and SNPeff (4.1 g), respectively. After 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^− 2) 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