Karen's Lab Notebook

I have been trying to address the question of what is different between super clone A and B. In doing this, I noticed that there were three scaffolds that initially looked like they might have an excess of fixed snps between A and B relative to their length, that all map to chromosome 10. These were scaffolds 2175, 1982, and 1927. I tried looking into the divergence between these super clones more, using a type of sliding window approach. First I identified all SNPs that were fixed between different D8 super clones (so homozygous ref in one super clone, and homozygous alt in another). I then scanned along the scaffolds with fixed differences in 2,500 bp chunks, and asked how many fixed snps are there within these windows, and then divided that by the 2,500bp. As I am writing this I realize a problem with this, in that if a scaffold was 3,000bp long, there would have been one 2,500 chunk, and then a 500 chunk, so some of these estimates will be low. But most windows should be ok. For no...

Fixed Alt Chr 1  Chr 2  Ch3 Chr 4 Chr 5 Chr 6 Chr 7 Chr 8 Chr 9 Chr 10 Chr 11 Chr 12 Heterozygous Chr 1 Chr 2 Chr 3 Chr 4 Chr 5 Chr 6 Chr 7 Chr 8 Chr 9 Chr 10 Chr 11 Chr 12  Prop Alt Scaffold 1982 Prop Alt Scaffold 2175

I have looked at fixed differences between super clones A and B before, but I realized I had been starting with a parsed set of SNPs, the SNPs that I had been using for PCA analysis. So pruned based on linkage and such. Thus I was underestimating the number of SNPs fixed between and and B. So I went back and started with all the SNPs. I then first looked at SNPs that are fixed between super clones A and B, regardless of what their frequency is in any other pond/super clone. I found 28,237 SNPs that are homozygous reference in super clone A and homozygous alternate in super clone B, and 54,000 SNPs that are homozygous alternate in super clone A and homozygous reference in super clone B. There are also 83,789 SNPs that are heterozygous in super clone A and homozygous reference in super clone B, and 63,908 SNPs that are homozygous reference in super clone A and heterozygous in super clone B. So there are quite a number of SNPs between these super clones. One other thing is that there are ...