Post date: Jan 14, 2020 12:49:31 PM
Tasks done today:
- start to read one review but could not finish it (lack of understanding) - Spatial Population Genetics, it is about time, Bradford and Ralf 2019
- estimating allele frequency - understand AC/AN:
AC = Allele Count - for each alternative allele, in the same order as listed
AN = Allele Number - total number of alleles in one SNPs
I have number at both extremes (close to 1 and close to 0) while I was only expecting numbers under .5 or .8. I think it is depending on which allele has been chosen as reference/alternative. One way to counteract this is to mirror the data? I decide to substract the value to 1 from all values >= 0.5 - it should take a 0.9 for example back to 0.1.
Graphs of allele frequency for SNPs with heteroZ below 0.8 or 0.5 can be found here.