@isaacovercast Thank you very much for your reply. I am indeed working with an endangered species that has very low genetic variability, but I wasn't sure if what I found is related to my organism or if did something wrong in my analysis. I was actually working with the .vcf file when I noticed this. I estimated the per site nucleotide diversity (pi) and noticed that from 32,123 sites, 91% had pi=0. I checked the genotypes of all my individuals in some of these sites and confirmed that they were all the same. So that's why I was confused, because I thought the .vcf file contained only the polymorphic loci.