Just after the completion of human genome sequencing, the mouse genome was determined prior to any other higher organisms. Many standard mouse inbred strains have been sequenced but quite a few gaps still remain as shown in Figure. Human genome reference sequences have already been revised in 2015 in order to fill the gaps as well as to finalize the structural variations like inversions, translocations, duplications and so forth. Accordingly, it becomes necessary to revise the mouse genome reference sequences as one of the most widely used model systems for, e.g., human diseases. Thus, RIKEN conducts the revision of reference mouse genome based on two big data of mouse genome sequences. One is a set of ultra-deep short-reads that was produced by the large-scale analysis of mouse genome and mutations supported by Genome Sciences. The other will be a newly produced set of one-molecule long-reads produced by a latest sequencing technology. Combining together, not only the gaps but also all the structural variations will be revised with the highest precision. RIKEN will make it open to public the assembled as well as original data. Thus, all researchers may further revise and/or add various annotations to the mouse genome reference.