missing homozygous minor allele

[Tina]

Hello, 

May I ask, when I did Data -> Numerical Genotype on my vcf file, I don't see any homozygous minor 0.0 in the output Probability file, only heterozygous 0.5 and homozygous major 1 for all taxa and sites.

I also saw this note "Reference probability computed by setting alternate minor alleles to the most common minor alleles"

Could anyone share some insights here? 

Thanks,

Tina