Forgive me if this is a dumb question but I assumed that the Average Heterozygosity was somehow related to the average distribution of frequencies seen for each allele in any given variation, i.e a AvHet close to 0.5 and a avHetSE lower than 0.1 would probably mean that that variation with 2 detected alleles would have a relatively balanced allele count for each like 0.45 for Allele A and 0.55 for Allele B.
Is my thinking flawed? I ask this because I filtered dbsnp137 using AvHet of >= 0.4 and avHetSE < 0.1 and I am getting loads of variations where 1 allele is clearly dominant with frequency count above 0.8.
I've tried to get my head around the maths for the AvHet calculation in http://www.ncbi.nlm.nih.gov/projects/SNP/Hetfreq.html but I admit defeat. I am not a Mathematician by training and could not make sense of it.