SR4R SnpReady for Rice
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)”.
Tools
-
Basic genotype processing
- Hapmap statistics
- Extract SNP genotype
- Extract flanking sequences
- Hapmap2ped
- Hapmap2vcf
- Hapmap2bgl
- Genotype imputation
- Population diversity analysis
- NJ tree builder
- Principle component analysis
- Population structure analysis
- IBS analysis
- ROH analysis
- LD analysis
- Theta pi analysis
- Tajima'D analysis
- Fst analysis
- Rice varieties classification and
identification
- Machine learning based classification
- Match and Identification
News & Updates
- SR4R version 1.0 is publicly accessible. (2019-06-18)
- DNA fingerprint analysis is implemented in SR4R. (2019-06-05)
- Subpopulation classification is implemented in SR4R. (2019-05-27)
- SR4R beta version is publicly accessible.(2019-05-05)
Publication
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