In looking at the mpox build and for B.1 samples I noticed that there are seveal OPG’s listed with multiple changes that I am unclear on interpretation. Using MPXV/AR-ANLIS037/2022 as an example, OPG153 lists a series of F->X changes. And the same is true for a few other OPG’s.
Additionally there are a few OPG’s with a “_dup” suffix, all with K->X changes listed.
What exactly are these notes capturing and do they have any impact on placement in the tree?
thanks for flagging this. These mostly correspond to parts of the genome that are masked in the alignment because they are low complexity, align unreliably, or because they represent a second copy of the terminal repeats. It is a bit unfortunate that they show up as changes relative to root – we’ll have to look into how we improve this. thanks again.