Let's say you compare 20 samples from Pop A with 20 samples from Pop B and the FST result is 0.1000. If you then compare any 10 samples from Pop A with the 20 samples from Pop B, the FST will always be lower by a significant amount, say to around 0.0950. Then if you compare the 20 samples from Pop A with any 10 samples from Pop B, the FST will always be higher, say to around 0.1050. If you compare any 10 samples from Pop A with any 10 samples from Pop B the FST result will be very close to 0.1000.
Is this a known issue?
