Download bulk data sets
SNP Genotype data from resequencing projects
DOWNLOAD data sets in the hapmap, plink (map, ped), or flapjack format:
- Huang X, et al Nat Gen 2010/Rice HaplotypeMap Project. 842,474 SNPs x 374 landraces, IRGSP4 coordinates. [ hapmap | plink | flapjack ]
- OryzaSNP Project: ~160,000 SNPs x 21 varieties, MSU6. [ hapmap | plink | flapjack ]
- Zhao et. al PLoS May 2010: 1536 SNPs x 395 varieties. A Rice Diversity study. MSU6.
hapmap | plink | flapjack ]
- Functional SNPs. Note: SNPs #2-15 are functional SNPs, and 6 of them are on the reverse strand (SNPs #2,4,5,6,9,10).
- Suppl data from pub: Sample/subpopulation information (Table S1), SNP marker info (Table S2)
- Gross B, et. al, Mol Ecol. Aug 2010 Rice grain color SNP diversity study, 633 SNPs x 143 rice accessions, chr12, MSU6. [ hapmap | plink | flapjack]
- Sweeney et al, 2007, Pericarp color study (Rc gene) with 440 germplasm accessions. [ phenotype_data ]
- Panzea: Maize Diversity Hapmap1, AGPv2, 1.6 million SNPs x 27 NAM founder lines. [ downloadable files coming soon
- Atwell et. al, Nature June 2010. Genotype, phenotype, association data. ~214,000 SNPs, 199 Germplasm, 107 Phenotypes [ hapmap | plink | flapjack (chr1 2 3 4 5) ]
- 2010 Project SNP Discovery: 637,522 SNPs x 21 ecotypes (incl. Col-0 reference), TAIR9. [ hapmap | plink | flapjack ]
- 2010 Project 250K SNP chip genotypes v3.04, ~214,000 SNPs x 1179 ecotypes, TAIR9. [ hapmap | plink | flapjack ]
- 1001 Genomes (WTCHG/Mott) from dbSNP, 2,698,797 SNPs, 17 ecotypes, TAIR9. [ hapmap | plink | flapjack (chr 1 2 3 4 5)]
FLAPJACK is a genotype visualization tool developed by the Plant Bioinformatics Group at the The James Hutton Institute. Gramene Diversity SNP datasets have been converted to Flapjack project files which can be downloaded above and loaded in to Flapjack running on your machine. Download Flapjack.
PLINK files are provided for those who wish to analyze our data in the PLINK whole-genome analysis toolset.
HAPMAP files are formatted in a standard developed by the International HapMap Project.
Complete MySQL database downloads
Download complete Diversity data sets can be downloaded as full MySQL database dumps from the Gramene FTP site. (Gramene Genetic Diversity databases are contained in filenames, 'diversity_*').