Using the MiSeq sequencer, we obtained a total read length of 2.79 × 109 bp from the total read number of 9.53 × 106 in Koshihikari Jukkoku_sd1, while a total read length of 1.92 × 109 bp was obtained from a total read number of 6.13 × 106 in Koshihikari. By mapping the read sequences obtained by NGS using Nihonbare genomic DNA as a reference, sequence coverage rates of 93.5% and 88.5% were attained for Koshihikari Jukkoku_sd1 and Koshihikari, respectively, while average depths were 9.17 and 7.29, respectively. Furthermore, vcf files of the entire genomes were prepared and the whole-genome sequence of Koshihikari Jukkoku_sd1 was compared with that of the virtual Koshihikari genome. As a result, three reads were obtained, including Jukkoku_sd1 from Koshihikari Jukkoku_sd1, while three reads of Sd1 were obtained from Koshihikari. The Sd1/sd1 locus (Os01t0883800-01) was localized at positions 38,382,385–38,385,469 from the end of the short arm of chromosome 1 in the Koshihikari genome. The difference observed between the Koshihikari_Sd1/Jukkoku_sd1 alleles was only one SNP from G to T in exon 1 of the GA20-oxidase gene (Figure 5), as reported by Sasaki et al. . In this study, the G to T SNP of the defective GA20-oxidase gene was localized at position 38,382,746 from the end of the short arm of chromosome 1 of Koshihikari. Using this scale of the NGS approach with a coverage of only 5×, the targeted SNP in Jukkoku_sd1 was successfully identified with three reads, with a cost reduced to 1/5 that of the ordinal whole-genome sequencing with a coverage of 30×.