Genome Variation Map: a platform for the analysis and integration of genomic variation

Abstract The Genome Variation Map (GVM; https://ngdc.cncb.ac.cn/gvm) serves as a public repository for genetic variation data. This version represents a major upgrade to GVM, integrating rigorously curated high-quality DNA resequencing data from a wide range of species and delivering significant enhancements over previous releases. Specifically, the current release encompasses ~2.14 billion standardized variants across 73 species and archives 898 genetic variation projects originating from 79 species, contributed by 180 organizations globally. Furthermore, GVM innovatively incorporates a public variant aggregation pipeline that consolidates in-house curated datasets, user-submitted data, and records from the European Variation Archive to generate comprehensive reference variant sets for each organism. A new module has also been introduced to provide deleterious variant annotations and population genetic selection signals based on population genetic analyses. Additionally, newly implemented online tools support population-specific haplotype analysis and cross-mapping between genome assemblies, serving as integral features of GVM. Collectively, this resource remains essential for archiving and utilizing genomic variation data and for catalyzing advancements in evolutionary biology, disease etiology research, and agricultural genomics.