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.

Start here → See example workflows
19,035 rice genomes
9,309 newly sequenced
5 platinum references
~57M variants
2.02M high-effect reg. variants
138 AlphaFold3 models

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.

Explore a gene or SNP

Genotypes, haplotypes, and allele frequencies for a region across all accessions.

SNP-Seek v3 →
Browse a genome

Gene 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 traits

Pre-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 download

Raw reads, full variant archives, and citable DOIs (NCBI / EVA / KAUST).

Archives & bulk →

How 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, chr3:31,031,753-31,041,563

    import 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

Cite this resource. Zhou Y. et al. Unity in Diversity: A Global Atlas of 19,035 Rice Genomes. Cell (in revision), CELL-D-26-01478. Full citation and data-availability details on the Cite & about page.