title: RiceVarMap: a comprehensive database of rice genomic variations.
abstract: Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Hu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Yao
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yidan
authors.initials: Y
authors.lastname: Ouyang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Wanneng
authors.initials: W
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Gongwei
authors.initials: G
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xingming
authors.initials: X
authors.lastname: Lian
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Xing
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Lingling
authors.initials: L
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China weibo.xie@mail.hzau.edu.cn.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
mesh_terms: D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D006239:Haplotypes; D054643:INDEL Mutation; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide