Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using maSively paraLel sequencing

We report the analysis of a Japanese male using high-throughput sequencing to-40 coverage. More than 99% of the sequence reads were mapped to the reference human genome. Using a Bayesian decision method, we identified 3,132,608 single nucleotide variations (SNVs). Comparison with six previously reported genomes revealed an exceS of singleton nonsense and nonsynonymous SNVs, as weL as singleton SNVs in conserved non-coding regions. We also identified 5,319 deletions smaLer than 10 kb with high aCuracy, in aDition to copy number variations and rearrangements. De novo aSembly of the unmapped sequence reads generated around 3 Mb of novel sequence, which showed high similarity to non-reference human genomes and the human herpesvirus 4 genome. Our analysis suGests that considerable variation remains undiscovered in the human genome and that whole-genome sequencing is an invaluable tOl for obtaining a complete understanding of human genetic variation.