RiceVarMap: A Comprehensive Database of Rice Genomic Variations

We constructed a database of rice genomic variations, Rice Variation Map (RiceVarMap, http://ricevarmap.ncpgr.cn). The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNP) and 1,214,627 insertion/deletions (INDEL) identified from low-coverage sequencing data of 1,479 rice varieties. The genomic variations were annotated based on MSU Rice Genome Version 6.1. The SNP genotypes of all varieties were imputed and evaluated, resulting in a missing data rate less than 1% and an estimated accuracy greater than 99%. The SNP genotypes of all varieties can be queried. In particular, the database provides a tool to compare any two cultivars and find out genomic variations between them. For each SNP/INDEL, allele frequencies within various sub-population and the effect of the variation are also listed. Users can search SNP/INDELs by identifiers of the SNP/INDELs or genomic regions, then filter SNPs by allele frequencies. Users can also identify large effect genomic variations that may alter the protein sequence of a gene by searching SNP/INDELs using the gene identifier as keyword. Moreover, the query results are available for users to download through our website. Such information is expected to be useful for identifying genetic variations and genetic improvement in rice.