Genetic Diversity Data Download

SNP Genotype data from resequencing projects

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Rice

Zhao K, et al, Nat Comm, 2011. Rice Diversity GWAS study. 413 diverse accessions, 44K SNP array, 34 phenotypes. MSU6 [ hapmap | plink | flapjack ]
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 ]

Maize

Panzea: Maize Diversity Hapmap1, AGPv2, 1.6 million SNPs x 27 NAM founder lines. [ downloadable files coming soon ]

Arabidopis

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)]