Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri

•Samba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior grain and cooking qualities.•Genome of SM was decoded and comparative genomic analysis using SNP-Seek and EnsemblPlantsv40 database revealed many novel alleles for grain quality.•Novel stop-gain mutations identified at several known loci, which may explain the observed weak biotic stress tolerance of SM.•Novel missense SNPs were mapped to genes that are associated with as many as 62 metabolic pathways.•Genomic resources described here are potentially useful in breeding programs for improved SM for grain quality and stress tolerance.