In this project, we use unified standard SNP-calling pipeline for SNP-calling.

We designed a powerful search engine for our variation database. Here we collected a great deal of information among the findings of rice genomic research into our database. Our search conditions are ingenious, which can help you determine appropriate constraints in order to locate the results you want precisely.

  1. From another point of view, you can restrict the variation itself, for instance, minor allele frequency, position and the variant type of the variation.

  2. Better and better, from our database, you can retrieve the information of the Gene annotation, Gene ontology, KEGG pathways, and so forth. Since variation makes a difference mainly in the coding region, of which the biological functions are vital, these information could really help a lot in your studies.

  3. Last but not least, we devised the search interface for the information from QTL (quantitative trait loci), trait ontology and GWAS (Genome Wide Association Study) results. These results are scattered in the literature and different kinds of websites based on outdated and puzzling genome versions, which is absolutely unhelpful to basic research and applied research in rice.

    You can find the (1)SNP information, (2)population diversity in the total samples and different groups, (3)genotype information of each accessions, (4)annotation information, (4)related gene summary and their (6)associated traits.

  1. RiceClustalW
  2. Population Genetic Analysis Toolbox
  3. GHA: Gene Haplotype Analysis