Welcome to SR4R

The SnpReady for Rice (SR4R) database presents four reference panels of SNPs and tools to satisfy different aspects of population genetics, evolutionary analysis, association studies and genomic breeding research for the rice (Oryza sativa) community.

Online analysis

Subpopulation classification

Assign rice varieties to five groups based on 38 barcodeSNPs using machine learning models for a provided hapmap file.

DNA fingerprint analysis

To match and identify rice varieties based on 38 barcodeSNPs for a provided hapmap file. The output is ordered by different site numbers(DSN) in the format of “Accession Name (group, DSN)”.


  • Basic genotype processing
    1. Hapmap statistics
    2. Extract SNP genotype
    3. Extract flanking sequences
    4. Hapmap2ped
    5. Hapmap2vcf
    6. Hapmap2bgl
    7. Genotype imputation
  • Population diversity analysis
    1. NJ tree builder
    2. Principle component analysis
    3. Population structure analysis
    4. IBS analysis
    5. ROH analysis
    6. LD analysis
    7. Theta pi analysis
    8. Tajima'D analysis
    9. Fst analysis

News & Updates


Yan J, Zou D, Li C, Zhang Z, Song S, Wang X. SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genomics Proteomics Bioinformatics.2020. [PMID: 32619768]

Development Team

  • BIG Data Center in Beijing Institute of Genomics, CAS
  • College of Agronomy and Biotechnology, CAU