dbSNP and dbVar: NCBI Databases of Simple and Structural Variations for All Organisms

The National Center for Biotechnology Information (NCBI) creates and maintains the dbSNP and dbVar databases that archive, process, display and report information related to germline and somatic variants from multiple species.  dbSNP houses short (<=50bp) genetic variations that include SNV, small indels, and microsatellites.  dbVar houses large (>50bp) genomic structural variations that include CNV, large indels, and complex variations.   The combined databases have over a billion variants from over 360 species, including many agriculturally important plants and animals.   The primary roles of both databases are to process submissions, archive the data, and distribute it for general use.  Each submission is assigned a database accession identifier (ss# in dbSNP or nsv#/esv# in dbVar) based either on flanking invariant sequence or locations asserted on reference sequences.  Because these assigned accession numbers are stable and can be cited in publications, they facilitate aggregation of additional information from many diverse organisms.  These submissions are then processed to aggregate information from multiple submitters (assign rs# in dbSNP), mapped and annotated on the latest genome assembly and NCBI Reference Sequences (RefSeqs).  The data are also integrated with other NCBI resources including Gene, PubMed, Nucleotide, Protein, ClinVar, BioSample, and BioProject.  dbSNP and dbVar data are made available in diverse ways: Entrez searches, study-specific reports, annotation on the genome, Sequence Viewer, and ftp downloads as BED, VCF, and other formats.  This presentation focuses on dbSNP and dbVar, summarizing current function and highlighting recent improvements.