NGS data has been widely and massively produced in recent years, but few of them were used in the plant breeding program. We applied public free bioinformatic tools on low coverage depth sequence data of seven Taiwan rice varieties to provide reliable SNP/indel information. This list of five Japonica and two Indica varieties were determined by local rice breeders. They consisted of different pedigree background and different genetic distances. Although these short reads sequence data could not be used to assemble the whole genome on a low coverage depth, about 5.5x to reference genome size, they still could be applied to find SNPs or small INDEL as useful markers for plant breeding program. In the present study, we will present how we pulled out the SNP and INDEL and followed by PCR confirmation using the NGS data.