**3. Results**

### *3.1. Whole Genome Sequencing and SNP Calling*

To analyze the genomic composition of the HYVs derived from *indica*–*japonica* crosses, the whole genomes of HYVs and four varieties were sequenced on the Illumina platform. A large number of short reads were mapped onto the reference Nipponbare genome and were then assembled into a consensus sequence. The number of sequence yields and the number of reads and mapping depths were varied. For example, a total of 66,464,246 reads of the Cheongcheongbyeo genome, corresponding to 9,991,040,272 bp (10 Gb), were generated, representing a 21-fold mapping depth. Nipponbare showed the largest number of sequence yields and number of reads and mapping depths (Table 1).

More than one million SNPs were detected in each of the eight HYVs and two *indica* varieties against the Nipponbare (*japonica*) genome. More than 90% of the SNPs were detected in the intergenic region. The smallest number of SNPs were in the 5 untranslated region (UTR). Two *indica* varieties, IR 8 and TN1, represented a relatively large number of SNPs, as compared to seven HYVs except for Minghui 63. Among the seven HYVs, Milyang 23 showed the smallest number of SNPs (Table 2).


**Table 1.** Basic sequencing statistics of the varieties used in this study.

Abbreviations are as follow: HYV—high-yielding variety, N (%)—percentage of skipped base, GC (%)—percentage of GC content, Q30 (%)—percentage of bases showing Phred quality score (Q) ≥ 30.

**Table 2.** Number and location of the SNPs in the varieties against Nipponbare pseudomolecule.

