We have genotyped a number of (most likely) double haploid plant samples and I've stumbled upon a skewed allele coverage depth on heterozygous SNPs. In optimal cases, each plant should mostly be identical to each other.
I've got quite a few SNP positions in which only 1 plant shows a heterozygous genotype call, while the others do not contain variation. These heterozygous calls then result in skewed allele coverage depth in which the alternative allele has quite a lower coverage:
Can I see these as false positive variation or would you consider these as true variation?