I'm returning to this field after a long haitus so please forgive the basic questions. Everything is confusing me right now as I can't remember anything and what I do remember I can't remember if it's right or not!!
What is the difference biologically between a SNP (found in 1% or more of population) and an infrequent variation (found in only a few individuals and isn't sequencing error)? Can you assign any significance to a variation that has a higher prevalence in the population? Can you say that because the SNP is found in more individuals it is more likely to have a phenotypical effect? Or perhaps you can say the infrequent variant is more recent that the polymorphism as it isn't as prevalent but may well become more esatablished in the population after more generations. Or perhaps you can't say anything at all.
If you find that a particular sequence variation occurs in many individuals in one population but is infrequent in a different population, can you make any conclusions about that?
If I wanted to understand more about this, what sort of area should I be reading about? Is it population genetics or evolutionary genetics or both or something else entirely?