Hi all, I would like to know how to interpret a variant calling result for diploids organism (e.g., yeasts).

Although several yeasts are diploid, their reference genomes registered at NCBI have only one allele sequence. So, I assume if I sequence the same strain with the reference, map reads, and call variants, I would find a heterozygous variation or no call.

However, when I tried the above strategy, I found homozygous variation as well. (The number of heterozygous is ~50000 and the number of homozygous is ~4000)

How should I interpret the homozygous variation? Since I am sequencing the same strain with the reference, at least one allele should be identical and all variants would become heterozygous variation.

If you have a similar experience and or know some clues, could you please teach me?

Thank you.