MR297 is a high-yielding commercial rice variety extensively cultivated in Peninsular Malaysia to this day, yet it lacks resistance against bacterial leaf blight disease. To mitigate this, ML-1 was derived from MR297 through acute gamma irradiation and has become a promising mutant line developed by Universiti Teknologi MARA Malaysia. During multiple field trials, ML-1 has shown improved yield potential and resistance during bacterial leaf blight outbreaks. However, comprehensive information on these genetic improvements remains limited. Here, to investigate the comparative genome-wide variations between the wild-type and the mutant line, we performed whole-genome resequencing on MR297 and ML-1 with Illumina NovaSeq™ 6000. Through bioinformatics pipelines, 97.6 and 98.4 million paired-end reads of MR297 and ML-1 were generated with sequence coverages of 39.0x and 38.8x, respectively, and were mapped to the Nipponbare reference genome (GCA_034140825.1). A total of 6,632,119 high-confidence SNPs and InDels in MR297 and ML-1 were identified and among these, 428,552 SNPs and 50,565 InDels were unique to the mutant. Variant functional annotation and effect prediction in both genotypes revealed 42,275 high-impact variants which were mapped onto 22,163 genes. Gene ontology analysis further screened for economically important genes and found 188 genes associated with disease resistance mechanisms and 333 genes associated with yield potential traits in the mutant. These data provide a basis for further analyses to validate putative variants influencing BLB disease mechanisms and may explain ML-1’s improved disease tolerance. These findings serve as valuable resources for the development of allele-specific molecular markers to facilitate marker-assisted selection (MAS) and enhance the precision of future rice improvement programs.