Hi, I have calculated the top 10 SNPs of their allele frequency differences between two populations (using 1000 genomes vcf data), but I am confused to draw a conclusion. What does a allele frequency difference between 2 populations mean? Geographical Drift? What else info can I get from the data?
By itself, differences in allele frequency mean very little. You can get different allele frequencies from any number of biological processes including drift and selection so it's hard to say what it means. You'll have to combine it with other data to ask any meaningful question.
You may consider inverting your design. Think about the biological question you want to answer first, then what data is suited to addressing that question rather than trying to figure out what you can ask from rather general data.
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version 2.3.6
Time for some reading: http://www.amazon.com/Population-Genetics-A-Concise-Guide/dp/0801880092