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. 2015 Jan;43(Database issue):D1018-22.
doi: 10.1093/nar/gku894. Epub 2014 Oct 1.

RiceVarMap: a comprehensive database of rice genomic variations

Hu Zhao  1 , Wen Yao  1 , Yidan Ouyang  1 , Wanneng Yang  1 , Gongwei Wang  1 , Xingming Lian  1 , Yongzhong Xing  1 , Lingling Chen  1 , Weibo Xie  2
Affiliations

RiceVarMap: a comprehensive database of rice genomic variations

Hu Zhao et al. Nucleic Acids Res. 2015 Jan.

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.

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Figures

Figure 1.
Figure 1.
Contents and functions of RiceVarMap. (a) Population structure of the 1479 rice accessions included in RiceVarMap. Labels denote the names of subpopulations and the number of accessions in the subpopulation. (b) The functions of RiceVarMap. (c) Haplotype network of S5 constructed using the tool ‘Haplotype Network Analysis’ implemented in RiceVarMap. Each circle represents a haplotype and the size is proportionate to the number of accessions with that haplotype. Branch length represents the genetic distance between two haplotypes.
See this image and copyright information in PMC

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