Center for Genomic Medicine, RIKEN analyzed the whole genome sequence of a Japanese male which had been genotyped by the International HapMap project. As a result, the research group identified over 3 million single nucleotide variations (SNVs), 5,319 deletions smaller than 10 kb as well as 3 million base pairs of novel genome sequences not found in the human reference genome (Press release from RIKEN).DDBJ Sequence Read Archive has released the sequencing data of the Illumina Genome Analyzer II used in this analysis under the accession number DRA000222.