I'm afraid that you don't know what the p-value is. The first thing about p-value is that it applies to populations, not to just plain numbers. If you have just two numbers (mean AF of your SNP vs. mean in 1kg database),then there is no discussion of having a p-value at all. Loosely speaking, the p-value says how much is the probability to draw samples in your population (of AF) if it came from other population (let's say of 1kg) - which loosely translates to how much your population (of AF of SNPs here) is different from other population (the 1kg AF, say) - the lower p-value means that the populations being compared are more certain to be different. You may find some useful posts on SE/SO regarding it, for example: https://stats.stackexchange.com/questions/166323/misunderstanding-a-p-value

Closing the discussion, if you need a p-value for your case, then you must have 1) either your whole population (=> the individual AFs in *all samples*, including 1kg) or 2) at least the mean and standard deviations of AFs.

BTW, what you need the p-value for?

Hi , To get a better statistic on your MAF you should get ExAC snp vcf http://exac.broadinstitute.org/downloads or gnomad http://gnomad.broadinstitute.org/downloads , if you are working on human genome. In this 2 databases 1000 genome are included.

Best

900Thank you the suggestion. Any idea how I can do a p-value calculation between my population's allele frequencies and the global allele frequencies?

Thanks

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