Identification of Y-linked scaffolds in the D. virilis (A) and human (B) genomes. The peak on the right corresponds to Y-linked scaffolds, and the peak on the left corresponds to autosomal and X-linked scaffolds. (Abscissa) Proportion of scaffold sequence not matched by female short reads (in percentage unmatched single-copy k-mers); (ordinate) number of scaffolds. (A) D. virilis genome, CA assembly (1186 scaffolds, 165 Mbp of sequence excluding gaps; see Methods). There are 807 Y-linked scaffolds (total sequence: 8.5 Mbp); only a few were known before. (B) Human genome, HuRef assembly (Levy et al. 2007; 4606 scaffolds, 2796 Mbp of sequence excluding gaps). There are 119 Y-linked scaffolds (total sequence: 18.4 Mbp); as expected, most of their sequence was already known to belong to the Y chromosome (Skaletsky et al. 2003).