I have aligned an unannotated genome assembly which consists only of scaffolds to the reference genome of a closely related species using LASTZ.
The stange result that I have obtained is that I see that a given scaffold from my genome assemly gets mapped to several chromosomes of the reference, for example, scaffold71 gets mapped, to different positions, of chromosomes 1, 2, 3, 14, 15, Z (avian sex chromosome).
My reference is hard repeat masked, my genome assembly is not if that could be the problem.
What could be the reason of such results and how could one go about it to solve this issue?
Thank you very much in advance.