Welcome to Rice Variation Map!

What's New

25 Jun 2014

A new design for webpage. Hope you like it.

25 Jun 2014

Added cloned gene symbol and explanation to the database.

09 Jun 2014

We added "What's New" page.

08 Jun 2014

Added a new function! Users can use keywords of gene annotation to search genes (Search for SNPs in Gene page), and click MSU gene ID can get detailed information.

Data source:

We collected low-coverage sequencing data of 1,479 rice varieties from two sources:

We sequenced 203 mini core collection of Chinese varieties and 330 worldwide varieties on the Illumina HiSeq 2000. High quality sequences of approximately one gigabase per variety were obtained, generating total 6.7 billion 90-bp paired-end reads.
We downloaded sequences of 950 rice varieties generated by Huang et al (2012, Nat. Genet. 44:32-39) from the EBI European Nucleotide Archive (accession number ERP000106 and ERP000729), which consisted of 4.6 billion 73-bp paired-end reads.

Data processing:

Reads were aligned to rice reference genome (Nipponbare, MSU version 6.1) using software BWA. SNPs were identified using SAMtools and BCFtools.Synonymous/non-synonymous SNPs and SNPs with large-effect changes were annotated based on gene models of the annotation version 6.1 of Nipponbare from MSU using SNP effector.

Database contents:

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.


This work was supported by grants from the National Natural Science Foundation of China (31100962, 31123009 and J1103510), the Research Fund for the Doctoral Program of Higher Education of China (Grant No. 20110146120013), and the Fundamental Research Funds for the Central Universities (2011PY068).

Comments or Questions?

For any questions please contact Hu Zhao ( zhaohu@webmail.hzau.edu.cn ).

The database is a "beta" version:

Both the database and the data are for pre-publication evaluation only, it may contain errors. We assume no legal liability or responsibility for any purpose for which the data are used. We are currently preparing papers on genome-scale analyses. By accessing these data, you agree not to publish any articles containing analyses on a whole genome or chromosome scale prior to publication by us. Please read our data usage policy in details.