The information commons for rice (IC4R) database is a collection of 18 million single nucleotide polymorphisms (SNPs) identified by resequencing of 5152 rice accessions. Although IC4R offers ultra-high density rice variation map, these raw SNPs are not readily usable for the public. To satisfy different research utilizations of SNPs for population genetics, evolutionary analysis, association studies, and genomic breeding in rice, raw genotypic data of these 18 million SNPs were processed by unified bioinformatics pipelines. The outcomes were used to develop a daughter database of IC4R – SnpReady for Rice (SR4R). SR4R presents four reference SNP panels, including 2,097,405 hapmapSNPs after data filtration and genotype imputation, 156,502 tagSNPs selected from linkage disequilibrium-based redundancy removal, 1180 fixedSNPs selected from genes exhibiting selective sweep signatures, and 38 barcodeSNPs selected from DNA fingerprinting simulation. SR4R thus offers a highly efficient rice variation map that combines reduced SNP redundancy with extensive data describing the genetic diversity of rice populations. In addition, SR4R provides rice researchers with a web interface that enables them to browse all four SNP panels, use online toolkits, as well as retrieve the original data and scripts for a variety of population genetics analyses on local computers. SR4R is freely available to academic users at http://sr4r.ic4r.org/.
IC4R（Information Commons for Rice）数据库收集了5152个水稻样本的1800万个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）。如此大规模的原始基因组变异图谱中包含大量的基因型缺失和位点冗余，并不能直接用于作物遗传育种研究的不同领域。为了提高基因组变异图谱的质量、易用性和通用性，需要构建由不同密度的高质量的SNP位点组成的分级基因组变异图谱。为满足水稻群体遗传学、进化分析、关联分析和基因组选择育种等方面的不同研究目的，我们对包含1800万个SNP的原始基因型数据进行统一的生物信息学处理，用于建立水稻IC4R-SR4R（SNP Ready for Rice）子数据库。SR4R数据库提供了4套分级基因组变异图谱，分别为经过数据过滤和基因推断后的2,097,405个hapmapSNPs，基于连锁不平衡去冗余后筛选出的156,502个tagSNPs，基于选择性清除扫描获得1180个fixedSNPs，以及基于DNA指纹模拟筛选出的38个barcodeSNPs。SR4R数据库不仅提供上述水稻分级基因组变异图谱数据的基因型信息查询和下载，还提供了18个用于本地分析的小程序，以及两个在线的基于机器学习的水稻亚群划分和品种预测的小工具。SR4R数据库有助于推进水稻遗传育种研究，其网址是http://sr4r.ic4r.org/。





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