Now I’m second-guessing myself again (third-guessing?).
In this 2016 article in ARJ, Jeanson draws a distinction between the AFS and the variants present in each individual:
To clarify, within the world-wide human population, over 84 million total SNV sites have been identified (1000 Genomes Project Consortium et al. 2015). Rare variants, by definition, represent most of these 84 million sites. Since common variants would be present at identical sites in a variety of different individuals, common variants would constitute the minority of sites—they show up frequently but add little to the total number of different sites. By contrast, within each individual, only 3.5–4.3 million SNVs exist on average, and the vast majority of SNVs (>80%) within a single individual are common variants (1000 Genomes Project Consortium et al. 2012, 2015). Thus, within each individual, >80% of the nuclear SNVs (80% by the “common variant” criterion; >98% by Fig. 3B) are due to inheritance of alleles that arose via fiat creation during the Creation Week in Adam and Eve, and a small but significant minority of nuclear SNVs within an individual are due to mutations since Creation.
This seems to suggest that I was right (yay?) earlier when I said:
Or am I mistaken in trying to compare these 2 things, because one is the AFS across a whole population while the other is the proportion of variants separating 2 individuals in a population?
Anyone else want to weigh in on this?