Unity in Diversity
A Global Atlas of 19,035 Rice Genomes
One resource, five platforms — explore, query, and download. This guide shows how to access the data efficiently: APIs, precomputed summaries, and runnable example workflows.
I want to…
Choose your path
Six entry points into the atlas — pick the task you have in mind and we'll route you to the right platform.
Genotypes, haplotypes, and allele frequencies for a region across all accessions.
SNP-Seek v3 Browse a genomeGene models, variants, and predicted effects in an Ensembl-based browser + REST API.
GrameneOryza Climate ↔ genome (G×E)Genotype–environment associations across landraces.
Oryza CLIMtools Predict 5 traitsPre-trained models predict agronomic traits from genotypes (Docker / Colab).
Code & Models Query efficiently (API)Stream a locus across 19,035 genomes with tabix — no full download.
API & programmatic Bulk downloadRaw reads, full variant archives, and citable DOIs (NCBI / EVA / KAUST).
Archives & bulkHow the platforms fit together
One dataset, five access points
Quick start
Three ways in
# Resolve a gene to coordinates (GrameneOryza / Ensembl REST)
curl -s "https://rest.ensembl.org/lookup/id/Os03g0752800?content-type=application/json"
# -> MADS14, chr3:31,031,753-31,041,563import oryza19k as o19 # the access cookbook (notebooks/oryza19k.py)
gene = o19.lookup_gene("Os03g0752800") # MADS14 via Ensembl REST
bench = o19.summary_table("benchmark") # precomputed model x trait table
preds = o19.predict_trait(genotypes, "hdg_80head") # pre-trained model# Stream ONE locus across all 19,035 genomes — no full download
tabix -h https://<public-host>/19K-RGP/IRGSP-1.0/19K-RGP.IRGSP-1.0.snps.vcf.gz 3:31031753-31041563