GeneScanner: profiling genetic variation across bacterial populations

Rapid, low-cost genome sequencing has transformed microbiology, advancing efforts to link genetic and phenotypic variation. In laboratory settings, genome-wide functional screens of reference strains are revealing genes and mechanisms underlying important phenotypes. Simultaneously, population-scale comparative genomics describes the breadth of natural genetic and phenotypic diversity across lineages. These approaches provide complementary but contrasting information. Whereas laboratory studies offer causal understanding within simplified systems, population-level analyses capture ecological realism but are largely limited to detecting associations rather than cause-and-effect relationships. Linking laboratory-derived mutations to natural population variation remains challenging, particularly for researchers lacking bioinformatics expertise. Here, we present GeneScanner, a user-friendly tool that facilitates analysis of gene- and protein-level variation across large bacterial genome collections. GeneScanner detects genetic variation and amino acid substitutions in homologous sequence and supports genotype-phenotype association studies. By bridging laboratory functional genomics data with genomic diversity across natural populations, GeneScanner enhances functional interpretation of microbial variation in the real world, supporting research in antimicrobial resistance, virulence, and pathogen surveillance.