The application of next generation sequencing technologies allows us to discover the high levels of DNA polymorphism throughout a genome, e.g., single nucleotide polymorphisms (SNPs), and insertions and deletions (InDels). We performed whole-genome resequencing of a Korean rice cultivar (cv. Donganbyeo) and then obtained the sequences of covered 366,042,872 bp (96.63%) with average mapped read depth of 34.17 on 382,788,128 bp of the Japanese cultivar genome (cv. Nipponbare). We characterized the polymorphisms of 173,711 SNPs, 295,334 insertions and 40,642 deletions based on the comparison of both genomes. About 11.5% and 17.8% of the annotated total SNPs were presented in the regions of 1kb upstreams and genes, respectively. The annotated InDels in gene regions were similar with 15.5% insertion (4,588) and 15.9% (5,100) deletions, but not in 1kb upstream regions with 9.0% insertion (2,662) and 14.3% deletions (5,100). In addition, the Korea rice genome sequences were mapped on individual chromosome, resulted that SNPs were shown with different frequencies from each chromosome. The InDels distributions on individual chromosomes exhibited similar pattern as compared to those of SNPs. Some gene families such as NB-ARC (NB-LRR), F-box, RLK (serine/threonine protein kinase) and Zinc-finger (RING) for SNPs occurred the similar pattern with those of Arabidopsis. These results might be useful for better understanding the genome structure and genetic diversity of the Korean rice cultivars.