I figured out the chromosome painting!

Ok, I finally figured out what I was doing wrong with the chromosome painting. Here is the results for scaffold 1982 (the divergent one I focused on in lab meeting). First looking at all ponds (D8 and surrounding, D10, and W ponds). Super clone A clones are on the bottom, then super clone B clones are next.

Now focusing on just the D8 and surrounding ponds. Again, super clone A clones are on the bottom, then super clone B clones are next. You can see that A and B are pretty divergent from one another. It also looks like a lot of the other clones are hybrids of the two (lots of green), while some of the others look like B. Not too many that look like A.

Similar graphs but now looking at another scaffold, first 5000 SNPs on scaffold 951, just for comparison. See a similar pattern, except clones that looked heterozygous or B in 1982, don't necessarily look the same for 951. Sometimes clones are heterozygous or B in both, but sometimes they are heterozygous in one, but B in the other. So showing that B and heterozygous SNPs are in large chunks, but do switch back and forth like one would expect for recombinant hybrids (not F1).

All ponds

D8 and surrounding

D8 and surrounding, scaffold 951, last 5000 SNPs (instead of first 5000).