Rice (species in gen. Oryza) is not only an important model organism for monocots but also the most widely consumed staple food for a large part of the world's human population (about 2.5 billion people). Recently, thousands of rice accessions have been re-sequenced, in which single nucleotide polymorphism (SNP) is an important molecular marker for rice breeding. So we collected almost all the public available re-sequenced rice accessions (5152), and identified about 18M SNPs against Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecule using unified standard SNP-calling pipeline.
Here we provide detailed annotation information of variations, including SNP consequence, gene function, etc.. It was also hyper-linked to other databases (e.g. dbSNP). We curated the SNP effects by integrating available genotype-to-phenotype association results. We developed a powerful 'Search Engine' and a multi-track 'Browser' for users to obtain desired information. Also, we developed three practical online tools, RiceClustwl, Population Genetic Analysis and Gene Haplotype Analysis, for users to do advanced data mining and analysis.