# 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.

Open SNP-Seek ↗ Jump to examples

## 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)

1. Open Search → Genotype and enter the gene `OsMADS50` (or a region).
2. Choose the reference (e.g. IRGSP-1.0) and a variety subset (e.g. XI).
3. Render the genotype matrix; click Compute local haplotypes to group accessions.
4. 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.