Question: what is the meaning of "consensus mutation"?
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gravatar for 2001linana
8 weeks ago by
2001linana20
2001linana20 wrote:

Hi. I read something like " Only 11 sites show polymorphism in >5% of sequences; yet two mutations, including the D64G mutation in Spike, have already become consensus." I was wondering, what is the meaning of "consensus mutation" then? Many thanks for your time and attention.

sequencing sequence • 166 views
ADD COMMENTlink written 8 weeks ago by 2001linana20
2

I believe when we perform a multiple sequence alignment, for each position the most frequent nucleotide can be called "consensus". So in this situation I guess more than half of the samples have this mutation.

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.9k

You mean the most frequent nucleotide is called "consensus".

ADD REPLYlink written 8 weeks ago by 2001linana20
1

Not necessarily. Sometimes we have positions where the different muations frequencies are not very infromative. Eg. A has a freqiency of 30%, c 25%, g 25%, t 20%. Instead of calling A a consensus, we put N in the consensus sequence.

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.9k

So, it is only called "consensus" if the frequency of this mutation site is more than 50%, as you have mentioned earlier.

ADD REPLYlink written 8 weeks ago by 2001linana20

As for everything in bioinformatics, there is no strict consensus on it...

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.9k

I see, because it is a vague subject.

ADD REPLYlink written 8 weeks ago by 2001linana20

Moreover, some computational logics in bioinformatic articles are lacking...

ADD REPLYlink written 8 weeks ago by 2001linana20

I absolutely agree with you, even though I am a part of this problem

ADD REPLYlink written 8 weeks ago by German.M.Demidov1.9k

haha... Hope we can discuss / cooperate more in the future about various topics. I'm mainly in the computational side currently.

ADD REPLYlink written 8 weeks ago by 2001linana20

You received answers in many of your previous questions. Please take the time to upvote and accept helpful ones.

ADD REPLYlink written 8 weeks ago by ATpoint44k
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