SNP-Seek v3
IRRI's variant-and-phenotype warehouse for the rice panels — genotypes, local haplotypes, allele frequencies, and accession passport/phenotype data, all queryable for a region across every accession at once.
README — what it is & what it hosts
The 19K-RGP release in SNP-Seek provides biallelic SNPs and small InDels (plus gVCFs) called against two references.
| Dataset | Reference | Access |
|---|---|---|
| 19K-RGP SNPs + InDels | Nipponbare IRGSP-1.0 (GJ) | viewer · bulk · API |
| 19K-RGP SNPs + InDels | MH63RS3 (XI) | viewer · bulk · API |
Interactive tools: genotype viewer, embedded JBrowse, gene-locus search, pairwise SNP comparison, allele frequencies, phenotypes, and subpopulation grouping.
Use this when… you want all-accession genotypes or local haplotypes for a small region (genes, QTLs < 500 kb), allele frequencies, or to tie genotype to IRRI passport/phenotype.
Tutorial — the genotype viewer (OsMADS50)
- Open Search → Genotype and enter the gene
OsMADS50(or a region). - Choose the reference (e.g. IRGSP-1.0) and a variety subset (e.g. XI).
- Render the genotype matrix; click Compute local haplotypes to group accessions.
- Read off the haplotype groups and export the table.
Workflow — genotypes + allele frequencies at a locus
Goal: get all 19K-RGP genotypes and per-group allele frequencies at MADS14 (chr3) in XI as a table. Region-query the locus → open the allele-frequency panel → download the genotype matrix (HDF5/CSV) → load in pandas. The region pull is small (seconds).
Examples
The SNP-Seek REST routes follow Mansueto et al. 2017; exact paths/params are being confirmed with the IRRI team. Until then, the equivalent query runs via remote tabix or the precomputed allele-frequency table.
# Genotype-by-region (schema per SNP-Seek II; confirm exact route with IRRI)
curl -s "https://snp-seek.irri.org/<api>/genotype?ref=IRGSP-1.0&chrom=3&start=31031753&end=31041563&varset=XI"import oryza19k as o19
# Documented, credential-free alternative today: stream the region with tabix
gt = o19.region_genotypes("Chr03", 31031753, 31041563, ref="IRGSP-1.0", source="tabix")Access & cite
Public Anonymous web UI; REST API (no login). Bulk downloads: VCF, HDF5, genotype matrices; 3K Rice Genomes Open Data on AWS.
Cite: Mansueto et al. (2017) Nucleic Acids Research — "SNP-Seek II"; Alexandrov et al. (2015) NAR.