Whole-genome sequencing and cataloguing of mutations at a single nucleotide resolution provides a useful functional genomics resource for researchers. To this end, we generated a whole-genome sequenced fast-neutron-induced mutant population in the model rice cultivar KitaakeX, which completes its life cycle in 9 weeks. In collaboration with the Joint Genome Institute and Hudson Alpha, we sequenced 3,200 mutagenized lines (45-fold coverage). Detailed analysis of 2,871 mutant lines reveals mutations in ~40,000 genes. Mutation types include single base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations in the mutant collection. To facilitate public access to this genetic resource, we established this open access database, called KitBase.