Question: Genotypes from different strand for same variant position
1
gravatar for first
14 months ago by
first30
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 • 412 views
ADD COMMENTlink modified 14 months ago by finswimmer13k • written 14 months ago by first30
3
gravatar for finswimmer
14 months ago by
finswimmer13k
Germany
finswimmer13k 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 14 months ago by finswimmer13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2002 users visited in the last hour