Data repository for the 3K RGP and OryzaSNP Project, hosted by IRRI

3K RG Data Usage License - read this first

IRRI Released Variety Panel

This is a set of 127 released varieties with genotype data available on SNP-seek and seed available from the IRRI Genebank. 

The genotype dataset is currently available in SNP-Seek under different genotyping datasets, enumerated in this table.

3k RG SNPs and Alignment files (IRRI-KAUST collaboration 2023)

SNPs and Alignment files for 16 reference genomes at AWS Public Data
SNP files (DOI:https://doi.org/10.25781/KAUST-12WKO , in VCF and PLINK2.0 format) for 16 reference genomes, at KAUST data repository
Mapping table for NCBI SRA accession IDs to 3kRG assay IDs

Full 3k RG Phenotype, SNP & indel Datasets release 1.2

3K RG morpho-agronomic data , MS Excel format

3K RG BAM files vs IRGSP1.0 and 93-11 (manifest)

Full 3K RG SNPs Dataset (includes multi-allelic SNPs)

3K RG 32mio SNPs , called vs Nipponbare MSU7/IRGSP1.0 genome, tabular format
32mio all SNPs README
3K RG & HDRA 160k high quality common SNP positions , tab-delimited text

3K RG Large Structural Variants release 1.0 (tar.gz)

Deletions called vs Nipponbare MSU7/IRGSP1.0 genome
Insertions, called vs Nipponbare MSU7/IRGSP1.0 genome
Duplications, called vs Nipponbare MSU7/IRGSP1.0 genome
Inversions, called vs Nipponbare MSU7/IRGSP1.0 genome
CNVs, called vs Nipponbare MSU7/IRGSP1.0 genome
Large SV dataset README

Biallelic 3k RG SNP & indel Datasets release 1.0

3K RG 2.3mio biallelic indel Dataset

3K RG 2.3mio biallelic indels, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
3K RG 2.3mio biallelic indels, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
3K RG 2.3mio biallelic indels, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
2.3mio biallelic indel dataset README

3K RG 29mio biallelic SNPs Dataset

3K RG 29mio SNPs, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
3K RG 29mio SNPs, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
3K RG 29mio SNPs, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
29mio Biallelic SNPs README

Effect of 29mio biallelic SNPs on Rice Genome Annotation Project rel 7 gene models

SnpEff results for 3K RG 29mio biallelic SNPs, VCF file

Subsets 3k RG SNPs release 1.0

3K RG 404k CoreSNP Dataset, all chromosomes

404K CoreSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
404K CoreSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
404K CoreSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
404K CoreSNP dataset README

3K RG 404k CoreSNP Dataset, split per chromosome, PLINK text-formatted zip files

Chr 1 (58 MB)
Chr 2 (54 MB)
Chr 3 (41 MB)
Chr 4 (57 MB)
Chr 5 (38 MB)
Chr 6 (41 MB)
Chr 7 (38 MB)
Chr 8 (49 MB)
Chr 9 (32 MB)
Chr 10 (32 MB)
Chr 11 (64 MB)
Chr 12 (43 MB)

3K RG 1M GWAS SNP Dataset, all chromosomes

1M GWAS-SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
1M GWAS-SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
1M GWAS-SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
1M GWAS-SNP dataset README

3K RG 4.8mio filtered SNP Dataset

3K RG 4.8mio filtered SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
3K RG 4.8mio filtered SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
3K RG 4.8mio filtered SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
3K RG 4.8mio filtered SNP dataset README

3K RG 18mio Base SNP Dataset

3K RG 18mio base SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bed file
3K RG 18mio base SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK bim file
3K RG 18mio base SNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK fam file
3K RG 18mio base SNP dataset README

Previous version 3k RG SNP Datasets

3K RG 990k CoreSNP Dataset (v0.4)

990K CoreSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK ped file
990K CoreSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK map file
990K CoreSNP dataset README

3K RG 6.5mio filtSNP Dataset (v0.4)

3K RG 6.5mio filtSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK ped file
3K RG 6.5mio filtSNP dataset, called vs Nipponbare MSU7/IRGSP1.0 genome, PLINK map file
3K RG 6.5mio filtSNP dataset README

3K RG Old Subset SNP Dataset (v0.2.1)

3K RG 365K SNP subset (formerly named CoreSNP v2.1), called vs Nipponbare MSU7/IRGSP1.0 genome, tarball PLINK file

Publication Datasets

Wang et al. 2018. Nature Communications 9:3519 (DOI: 10.1038/s41467-018-05538-1). RICE-RP imputed dataset of 5.2M SNPs for 4591 samples from 4481 genotypes.
Sanciangco, M. et al. submitted 2018. Discovery of genomic variants associated with genebank historical traits for rice improvement: SNP and indel data, phenotypic data, and GWAS results
Dilla-Ermita et al, Rice 2017 10:8 (DOI: 10.1186/s12284-017-0147-4), BLB GWAS dataset, 248 entries X 40,840 SNPs zipped hapmap format
Dilla-Ermita et al, Rice 2017 10:8 . Sample / accession names, CSV format
Raghavan et al. 2017. DOI: 10.1534/g3.117.042101, MAGIC SNP Genotype dataset, zipped hapmap format
Raghavan et al. 2017. DOI: 10.1534/g3.117.042101, MAGIC SNP Genotype dataset, zipped VCF format

Legacy OryzaSNP Datasets

SNP dataset from Nipponbare MSU r6 genome, flapjack format
SNP dataset from Nipponbare MSU r6 genome, hapmap format
SNP dataset from Nipponbare MSU r6 genome, plink format
100kb introgression score, MS Excel format