Heterozygous SNPs: Coverage distribution.

Question

[Coryza]

Hi,

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:

0/1:8,2
0/1:11,3
0/1:8,3
0/1:16,4
0/1:6,2
0/1:17,6
0/1:19,5

Can I see these as false positive variation or would you consider these as true variation?

[JC]

Some of the SNPs will be real but are individual/personal SNPs (only presented in one individual) others will be simply errors/noise in your variant calling. Individual SNPs are true variation source but not they are not significant unless are fixed in your population. So, depends on your biological questions to consider them or not.