I am calculating the proportion of heterozygous loci per individual using the next simple formula:
number of heterozygous loci/number of genotyped loci
I am using SNPs calls from illumina data and my values are close to 0.5. However these lines are supposed to be maize homozygous lines. The genotype calls came from 8 individuals. I had observed before that the proportion of heterozygous sites depends on the population and individuals used. However, it is possible to get such high values from inbreed lines? I am using ~38 M of sites. I am looking for an explanation for this and I begging in to think if the data is ok.
This data was processed in the same way for other heterozygous individuals and inbreed individuals and I get results of ~0.4 for the heterozygous individuals and 0.09 for the inbreed lines. Do you have suggestions about this?