Figure 5.

Proposed organization of the PWK/PhJ Y-linked duplication. X-linked segments involved in the duplication are shown in their position in C57BL/6J (mm10 assembly) in the top panel. Breakpoint coordinates and selected annotations are shown in the middle panel. The bottom panel shows alignments of breakpoint-spanning contigs to the PWK/PhJ X chromosome (which is near-identical to C57BL/6J), along with one possible reconstruction of the Y chromosome consistent with copy-number and alignment constraints. $d_{XY}$, absolute sequence divergence between X- and Y-linked copies of the pseudoautosomal region (PAR).