Question: Genotypes from different strand for same variant position
1
gravatar for first
5 weeks ago by
first20
first20 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 • 159 views
ADD COMMENTlink modified 5 weeks ago by finswimmer8.9k • written 5 weeks ago by first20
3
gravatar for finswimmer
5 weeks ago by
finswimmer8.9k
Germany
finswimmer8.9k 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 5 weeks ago by finswimmer8.9k
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