Fig. 4
Manhattan plots from microbial GWAS aiming to detect accessory genes and coregenome variants of Salmonella enterica subsp. enterica serovars (n = 440) associated with avian, bovine, swine and fish sources. Strains from both potential mono- and multi-animal sources were considered as having phenotype 1 and others strains (i.e. mono-source with a different animal) as having phenotype 0. The accessory genes were sorted by frequency and the positions of coregenome variants are in accordance with the reference genome of Salmonella Typhimurium LT2 (NCBI NC_003197.1). The blue and red lines (− log10(observed p-values)) correspond to the genome wide significance from human GWAS and polygenicity with regard to Quantile-Quantile (QQ) plots from microbial GWAS (i.e. p < 1 × 10− 2)