Question on heterozygosity

Question

[Lemonhope]

Hey everyone

I have a question regarding heterozygosity scores. Let me first tell you what I did:

I called SNPs for a diploid population via dDocent, filtered SNPs and was left with a filtered VCF file. I then used the stacks populations program (no smoothing or bootstrapping, no idea what those are) to generate population level statistics on the population as a whole (popmap consisted of only 1 specified population, i.e. SAMPLE\tPOP1). So I had several stats for each SNP of the population in the form of tsv files.

I then started plotting my tsv files in R to get an idea of my data and I notice that there were several observed heterozygosity scores where the heterozygosity was zero (Hobs = 0).

My question is how do I interpret this ? How can a SNP be called if it is homozygous across all individuals?

Thank you in advance for you aid,

Lemonhope

Answer 1

[Michael]

SNPs are called relying on a reference genome. Therefore, a homozygous will be detected in loci that are different from the reference but identical between the organism's chromosomes. In a diploid organism, a homozygous non-reference genotype will be encoded as 1/1 in the VCF file.

If the genotype differs between chromosomes, the variant is called heterozygous (e.g. given as 0/1). The heterozygosity is a measure of the general variability between chromosomes. Heterozygosity may be affected by and reflect population structure and history.