The Simons Genome Diversity Project (SGDP) dataset reports high-quality genomes from 300 individuals across 142 diverse populations, including at least 5.8 million base pairs not present in the human reference genome. The analysis reveals key features of human genome variation, such as an acceleration of mutation accumulation by about 5% in non-Africans compared to Africans since divergence. The study shows that some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the onset of behavioral modernity. It also demonstrates that indigenous Australians, New Guineans, and Andamanese do not derive significant ancestry from an early dispersal of modern humans but instead share ancestry with other non-Africans. The SGDP dataset highlights the incompleteness of current catalogs of human variation and provides insights into the structure and history of human genetic diversity.The Simons Genome Diversity Project (SGDP) dataset reports high-quality genomes from 300 individuals across 142 diverse populations, including at least 5.8 million base pairs not present in the human reference genome. The analysis reveals key features of human genome variation, such as an acceleration of mutation accumulation by about 5% in non-Africans compared to Africans since divergence. The study shows that some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the onset of behavioral modernity. It also demonstrates that indigenous Australians, New Guineans, and Andamanese do not derive significant ancestry from an early dispersal of modern humans but instead share ancestry with other non-Africans. The SGDP dataset highlights the incompleteness of current catalogs of human variation and provides insights into the structure and history of human genetic diversity.