Recombinant with extra samples: XAF

[hyanwong]

I thought it worth opening an issue for XAF, of which we have only one sample in the ARG. However, it does correspond to a recombination node (in pink below), and there are a large number of other samples (not designated as recombinants by Viridian) that also depend from this RE node (all are shown below). The pink/black clusters are the misalignable deletions e.g. shown in the recombination schematic below the subgraph here.

[hyanwong]

My guess is that there is a real recombination here, but it's not easily spotted by other methods because they require a number of distinctive mutations (the ones on the edge leading to the single XAF sample) to be able to identify the breakpoints.

It would be more interesting if we had more than one XAF sample, of course. But it might nevertheless be useful for Kat to look at some of those other BA.2 labelled samples (e.g. ERR9565786, SRR20344713, ERR9695062, ERR9760974, or ERR9755541) to see if they do look like reasonable recombinants. Here's the same plot with the strain IDs (although many overlap so are not visible)