Which genome regions were the original HGP plans mainly designed to sequence?

The original Human Genome Project plans were mainly designed to sequence euchromatic regions.

Euchromatin is the relatively open, gene-rich portion of chromosomes. It contains most known genes and is generally less dominated by long, nearly identical repeat arrays, making it more tractable for the cloning and sequencing methods available in the 1990s.

The early public draft therefore focused on the euchromatic portion rather than promising an immediately complete sequence of every base. The 2001 working draft covered about 90% of euchromatin, but still contained roughly 150,000 gaps. The HGP’s 2003 completion milestone likewise referred chiefly to the gene-containing euchromatic sequence.

A common mix-up is treating euchromatin as synonymous with coding DNA. Euchromatin includes genes, but also includes introns and many regulatory and noncoding sequences. Heterochromatin, especially around centromeres and chromosome ends, was harder to clone, map, and assemble because of its dense repetitive structure. Those regions required later technologies and projects to resolve more fully.