9.4. How are the homozygous and heterozygous calls determined?
The meaning of the columns in a variant track, including Zygosity, are covered in the manual here:
After variants are called by one of the variant detection tools, the "Zygosity" column in the variant output table reports if there is only one variant at that position (homozygous), or more than one (heterozygous). Thus, the status of a variant as homozygous or heterozygous in the Zygosity column reflects the parameters and filtering used when the variant calling was run, as these factors affect what will or will not be called as a variant.
In other words, even if there are several different bases in the reads at a position, if only one variant was actually called for that position, the variant zygosity value will be marked as Homozygous in the output variant table.