From the Science article: "However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs de

From the Science article: "However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished or incorrectly assembled (5)." Looks like there were "gaps" in the sequence due to technical limitations associated with the original sequencing methods and the authors have filled in those gaps. I haven't read the full paper, though.