Looking at fixed SNPs - other ponds

OK. Following up on the previous post regarding the distribution of SNPs that are fixed between super clones A and B. Now I am going to look in other ponds not in the original post. First, for what it is worth, I will look at the other ponds near D8, Doily (not pooled), D Ramps, and D Cat. For each of these three I only have sequences from five individuals, so the sample size is not high. Here is what I get.

D Oily April 2017 Hom Ref A (artificial pool)

 D Oily April 2017 Hom Ref B (artificial pool)

This looks pretty similar to what we see in the pooled D Oily sample taken in May, which is comforting.

D Oily May 2017 Hom Ref A

 D Oily 2017 May Hom Ref B

Now looking at D Ramps and D Cat. These look more multi-modal. Perhaps a bit more like D8?

D Ramps 2017 April Hom Ref A

D Ramps 2017 April Hom Ref B

D Cat 2017 April Hom Ref A

 D Cat 2017 April Hom Ref B

Out of curiosity I also looked at average heterozygosity for each of the 5 D Oily, D Ramps, and D Cat clones. They are all pretty heterozygous, especially Oily and Ramps.

 D Oily 2017 April

D Ramps 2017 April

D Cat 2017 April

Now looking at D10. First in 2012. Clearly multimodal.

D10 April 2012 Hom Ref A

 D10 April 2012 Hom Ref B

Then in 2016. Overall pretty similar shapes as seen in 2012. 

D10 2016 April Hom Ref A (artificial pool)

D10 2016 April Hom Ref B (artificial pool)

I also looked at heterozygosity in D10 2016. Lower heterozygosity than in D Bunk 2017 or in D8 2016.

I then started looking at ponds that are even farther away. Here are B1 and Bag. There does not appear to be any multimodality. I looked at all the ponds. And while there was some variation in the frequency of reads between 0 and 1, they all essentially looked like the graphs for B1 and Bag, where there are strong peaks and 0 and 1, and just an even smear in-between (no multi-modality).

 B1 2012 April Hom Ref A

B1 2012 April Hom Ref B

B1 2012 April Hom Ref A

Bag 2012 April Hom Ref B