The Hidden Pattern of Variation: Mapping SNP Landscapes across Mammalian Genes

Background : Single nucleotide polymorphisms (SNPs) represent the most abundant form of genetic variation in mammalian genomes and serve as critical markers in evolutionary, functional, and clinical genomics. Despite their extensive use, the distribution of SNPs across genic regions, particularly between exons and introns, remains uneven and not fully characterized across species. Results: Here, we explored the counts of SNPs in consecutive exons and introns of the human, bovine, and swine genomes, analysing 18,448 human, 19,657 bovine, and 17,342 porcine protein-coding genes (encompassing 41.8 million, 69.2 million, and 23.9 million polymorphisms, respectively). The three species demonstrated a consistent, non-random pattern - excess of SNPs in the first and the last exon as well as the excess of SNPs in the first few introns, especially the 1 ^st one. Conclusions: The distribution of single nucleotide polymorphisms among introns and exons appears to be not only highly nonuniform but also exhibits a very consistent pattern across mammalian genomes. This observation reflects the distinct functional roles of consecutive exons and introns within a gene.