Fig. 1

Hi-C chromosome conformation capture sequencing generated a single Y chromosome scaffold. a The contact matrix shows an enrichment of interactions between contigs in close proximity along the diagonal. Contig boundaries in the assembly are denoted by the black triangles along the diagonal. b Sanger sequenced BAC inserts that align concordantly throughout the scaffold are shown, with BACs that spanned gaps between contigs in orange, BACs that extended into, but did not span gaps in purple, and BACs that were contained completely within an individual contig in green