3K RG data
The most comprehensive resource for re-sequenced rice genomes to-date is the 3,000 Rice Genomes project, a collaborative effort from BGI-Shenzhen, the Chinese Academy for Agricultural Sciences (CAAS), and IRRI. The published datanote on the 3K RG dataset (The 3,000 rice genomes project) is available in GigaScience Journal.
3K RG at AWS: The Amazon Public Data program is hosting the 3K RG dataset (alignment to 5 published rice genomes, raw SNP and small indel calls from these alignments) , providing cloud-based infrastructure to make the dataset accessible and useable by geneticists and breeders.
3K RG at DOST-ASTI: In collaboration with the Philippines’ Department of Science and Technology Advanced Science and Technology Institute , the 3K RG analyzed data could be downloaded their data storage service — COARE Data Catalog. The COARE Data Catalog is a web-based research repository that hosts a number of research datasets. Also, it offers a web interface to search and access research datasets. The 3kRG dataset is hosted in the COARE Data Catalog. To access the dataset, visit https://asti.dost.gov.ph/coare/datahttps://asti.dost.gov.ph/coare/data and register for an account.
Another resource with genotype information for 700,000 SNPs from a diverse set of rice accessions (among other datasets) is the NSF ricediversity.org (McCouch et al, 2016) with > 1,600 genotyped accessions . The list of the accessions for this project is available here.
Databases on the web
1. SNP-Seek : Hosts the complete genotyping information for the 3K RG Project and other projects, as well as associated analyses tools, from IRIC.
2. RMBreeding : SNP and InDel database loaded with 3K RG data, from Rice Molecular Breeding & Molecular Genetics Group, Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences