I am currently trying to see which SNPs from a GBS project I'm working on convert and overlap known human SNPs. We had to do a Lift-Over from PapAnu2 to Hg19, then Hg19 to Hg38. When looking at the results, I noticed that in some cases multiple unique baboon genome locations converted to a single human location. I'm curious why this would happen and what it means, thanks.
The best way to understand the mappings is to view the Conservation track in the UCSC genome browser for these regions. Expand the track to full, review the track details (different "levels" of what can be thought of as syntenic regions are defined), then interpret from there.
My guess is that papAnu2 is not as finished as hg38. Redundant (overcalled) SNPs on Baboon are falling out during the conversions. But double check. If you find a data problem, report it to UCSC and they'll be able to help/sort out the issue.
Thanks, Jen, Galaxy team