Radiation-induced?mutation?has?been?efficiently?used?for?rice?germplasm?innovation.?In order?to?characterize?its?molecular?mechanisms,?whole?genome-wide?sequencing?was?performed?to?analyze?the?variations?in?γ-radiation-induced?rice?mutant?Xiangfu 1821?and?the?wildtype?Huanghuazhan. Compared with the reference R498, a total of 758?215 and 799?434 single nucleotide polymorphisms (SNPs), 142?313 and 147?686 insertions/deletions (InDels), 16?775 and 18?382 structural variations and 16?614 and 17?658 copy number variations were identified in Huanghuazhan and Xiangfu 1821, respectively. The ratio of transitions to transversions was ～2.5 in Huanghuazhan and Xiangfu?1821, the transitions was the main type. There was a greater number of shorter InDels than longer InDels, suggesting that point mutation was the dominant type of mutations in Huanghuazhan and Xiangfu 1821. Copy number reduction was the main copy number variation type of Huanghuazhan and Xiangfu 1821. Through?an?integrative?analysis?of?sequence?variations?between?Huanghuazhan?and?Xiangfu 1821,?we?identified?86?163?SNPs?and?88?777?InDels. The genes that included SNPs between Huanghuazhan and Xiangfu?1821 were used for GO analysis. Among the 3 092 candidate genes, 70% of them were involved in biological processes. These results will help to understand the phenotype of Xiangfu 1821 and provide novel insights into mechanism of the mutation breeding.