High-performance sequences are generating increasingly comprehensive catalogs of crop genetic variation. To make optimal use of this vast collection of data for research purposes, a robust and reproducible analytical pipeline discipline is required that is capable of accurately detecting and favoring variants. The entire genome sequencing data from the rice variety Nang Thom Cho Dao was analyzed using the appropriate bioinformatic pipeline. A total of 21 million reads with 6,6 GB of data were analyzed. SNPs and indels from the Nang Thom Cho Dao genome were found to be variable when compared to the Nipponbare reference rice genome. The result showed that the novel Indel of BADH2 gene in Nang Thom Cho Dao genome. The study will contribute valuable information to the development of genetic markers for rice breeding strategies using Nang Thom Cho Dao rice varieties.