For the accurate variation calling, we prepared subset of rice genome with ApeKI restriction sites. We searched the ApeKI sites in the genome and split it into fragments by the recognition sites. The subset of genome fragments smaller than 2kb were collected. The GBS short reads were mapped to the subset genome using software BWA \cite{Li_2009} and the genotypes of population were determined into homo- and heterozygous genotypes by SAMtools genotyping statistics with default parameter \cite{Li_2009a}. For cross-validation, parent lines were WGSed to compare allele contents for each locus with GBS results and we only selected the genomic positions for further analysis if GBS and resequencing results are agreed each other.