Off of dbSNP, it annotates with a couple of flags:
##INFO=<ID=G5A,Number=0,Type=Flag,Description=">5% minor allele frequency in each and all populations">
##INFO=<ID=G5,Number=0,Type=Flag,Description=">5% minor allele frequency in 1+ populations">
##INFO=<ID=COMMON,Number=1,Type=Integer,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency.">
I'm trying to figure out what the relationship each of these have with each other and with the GMAF (global minor allele frequency), assuming there is a relationship.
I seem to find nearly every combination possible. Sometimes, GMAF will be below 0.03 yet G5 and G5A are both there. Sometimes GMAF is above 0.05, and neither flag is there. Sometimes I will see the G5 or G5A flags, but the COMMON flag is a 0 (which is bizarre to me and shows me how little I understand of what is going on. How can something be greater than 5% in population yet not greater than 1%). Sometimes COMMON will be 1, yet neither the G5 or G5A flag are there. etc.
Can someone explain the relationships between these for me?
Your question seems to be missing some content.
>... it annotates with ...
Might not be a great idea to start off with a pronoun when others have no idea what you're talking about.
Sorry, I was referring to dbSNP (when you do a batch submission to dbSNP). The "it" is referring to that output after that submission.