Question: Genotypes from different strand for same variant position
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3 months ago by
first30 wrote:

In terms of genotypes and strand information, would a sample genotype AG be equivalent to GA? And would genotype AG be equivalent to CT or TC for the same variant position?

strand genotype • 217 views
ADD COMMENTlink modified 3 months ago by finswimmer11k • written 3 months ago by first30
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3 months ago by
finswimmer11k wrote:

Describing a variant on a different strand is always confusing.

If you are just talking about the genotype, you have to create the reverse complementary sequence. This means you start reading your initial genotype from right to left and changes each base to it complement (A/T or G/C).

So the reverse complement to AG would CT.

If you take the position of the variant into account, it looks a bit different. Positions are always described on the forward (+) strand. And if you describe an interval, you always starts with the lower position. So e.g. you have a variant AG on the forward strand starting on position 5, the equivalent description on the reverse strand would be TC starting on position 5 as well. You see I just created the complementary sequence and not the reverse complementary.

fin swimmer

ADD COMMENTlink written 3 months ago by finswimmer11k
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