I have assembled the genome of a non-model organism - insect (de novo genome assembly) and performed read mapping to it. I am currently in the process of performing a variant analysis. For all the different variants detected (SNPs, InDels) the initial results shows that 98% of all the variants are heterozygous (ie more than one variant was called at that position) and 2% were called as homozygous (ie only one variant was called at that position).
My question is, is it plausible to have homozygote variants present, especially since its the same species and the same set of reads were used to produce both the assembly and used in the read mapping? Or is it an error that homozygote variants are being called? I am using the CLC genomics workbench v9 to call the variants
Please advise. Thank you.