The Human Genome Project’s finished sequence covered about 92% of the human genome in 2003. The missing portion was concentrated largely in heterochromatic regions, including centromeres and telomeres, which are especially repetitive and difficult to assemble accurately.
The international project began in 1990 and was declared complete on 14 April 2003, two years ahead of its original schedule. Its main goal was to sequence the euchromatic portion of the nuclear genome—the gene-rich regions that make up roughly 92.1% of the genome—not every base of human DNA.
The often-confused figure of 99% refers mainly to coverage of the euchromatic target, not the entire human genome. Scientists eventually completed the remaining difficult regions: a gapless sequence of the non-Y chromosomes was published in 2022, while the full Y chromosome sequence followed in 2023.