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/.

水稻信息共享(IC4R)数据库收集了 1800 万个单核苷酸多态性 (SNP)，这些单核苷酸多态性是通过对 5152 个水稻品种进行重测序而确定的。虽然 IC4R 提供超高密度水稻变异图谱，但这些原始 SNP 并不容易为公众所用。为了满足水稻群体遗传学、进化分析、关联研究和基因组育种中SNP的不同研究用途，这1800万个SNP的原始基因型数据通过统一的生物信息学流程进行处理。结果用于开发 IC4R 的子数据库——SnpReady for Rice (SR4R)。SR4R提供了四个参考SNP panel，包括数据过滤和基因型插补后的2,097,405个hapmapSNP、从基于连锁不平衡的冗余去除中选择的156,502个tagSNP、从表现出选择性扫描特征的基因中选择的1180个固定SNP以及从DNA指纹模拟中选择的38个条形码SNP。因此，SR4R 提供了一个高效的水稻变异图谱，它将减少的 SNP 冗余与描述水稻种群遗传多样性的大量数据相结合。此外，SR4R 为水稻研究人员提供了一个网络界面，使他们能够浏览所有四个 SNP panel、使用在线工具包以及检索原始数据和脚本以在本地计算机上进行各种群体遗传学分析。SR4R 可在 http://sr4r.ic4r.org/ 上免费向学术用户开放。