Gbs

[Jayakumar S]

Hi,
Can we be able to identify the heterozygous genotypes by GBS when we do compare with reference sequence?

Thanks
Jayakumar S

[SNPsaurus]

Typically GBS is performed at a very low coverage, in which case heterozygotes are not directly detected. The diploid genotype can be imputed from the existing data if the reference includes the full genotype of both parents in a cross, for example.

At higher coverage you would see the heterozygous genotypes at most loci, and miss a subset because of polymorphisms in one of the two cut sites or polymorphisms that create new cut sites at the locus being assayed. The level of this issue depends on the diversity of the population.

[Jayakumar S]

SNPsaurus,
Thank you for the response and the details.

Jayakumar S