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I can't find any article about the expected number of mismatches in alignment of two alleles of an assumed gene. Any reference or information about allele mismatch ratio (in a species or higher taxa) is appreciated.

suppose we have 10 alleles for a gene in a population. if we pick two of this alleles and align them, which number (percent) of positions are expected to be mismatches (not gaps and matches). Of course, I know that in conserved genes and domains mismatch number are lower and in different genes and species this numbers are different. I want some information from scientific resources talking about this numbers.

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    $\begingroup$ Maybe it's just me - but I am a bit confused about what you are asking. Do you mean the expected number of pairwise differences which separate two genes samples from a population (population genetics)? Or is it specifically about the error in nucleotide alignment (bioinformatics)? Or maybe neither? $\endgroup$ – user438383 Jan 31 at 10:38
  • $\begingroup$ @user438383 suppose we have 10 alleles for a gene in a population. if we pick two of this alleles and align them, which number (percent) of positions are expected to be mismatches (not gaps and matches). Of course, I know that in conserved genes and domains mismatch number are lower and in different genes and species this numbers are different. I want some information from scientific resources talking about this numbers. I add this comment to question for more explanation. $\endgroup$ – MySky Jan 31 at 10:55
  • $\begingroup$ I think the question needs to be more specific. There are plenty of resources dealing with sequence alignments, and, as the question correctly points out, it depends on the gene, the organism, etc. It is not obvious what one wants to know: how count the mismatches? How to estimate their frequency from the mutation rate and phylogeny? Something else? $\endgroup$ – Vadim Jan 31 at 14:21
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    $\begingroup$ Still not sure exactly what you mean, but this question might be what you need. $\endgroup$ – user438383 Jan 31 at 14:39
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I think that the question is difficult to answer in the current phrasing. However, I will show how it might be easier to answer by filling in some blanks and defining some terms.

I am going to define as an "allele" any nucleotide difference between two sequences. This is the molecular genetic definition more or less. I am further going to interpret "mismatch" as also including sequence gaps, as in the case of indels your alignment will include gaps. I am assuming that you are talking about aligned sequence differences, because you mention alignments. I am going to ignore the focus on "genes" because at the molecular level visible in alignments, alleles are not necessarily tied to annotated genes (even though they are usually introduced in that context).

So in this case, if you assume that most alleles consist of single nucleotide variants (probably not true, but a helpful simplifying assumption), you can deduce that nearly all "alleles" thus defined will differ from each other at a single nucleotide position. A larger and more complex genotypic difference (for example a microsatellite variant or a transposable element (TE)) will involve a proportionally larger number of mismatches (i.e. gaps).

Indeed, if we look at the wikipedia page for "allele":

At the lowest possible size an allele can be a single nucleotide polymorphism (SNP).[7] At the higher end, it can be up to several thousand base-pairs long.[8][9]

You might however mean something different. It's possible that the question is rather something like this:

How much segregating genetic variation of an organism (say humans) consists of single nucleotide variants (SNVs) vs. larger/more complex variants?

That's a somewhat different but much more answerable question. It is unfortunately limited a bit by our ascertainment bias in favor of SNVs, which are just easier to find. But the best estimates that I'm aware of suggests that there are probably slightly more microsatellite variants than SNVs, and some work suggests possibly a similarly large number of large-scale repeat variants (such as TEs).

I can imagine yet another interpretation, which might be something like:

If we align two (or 10, or however many) homologous sequences of defined length drawn from a natural population of an organism (say humans), at how many positions can we expect the aligned portion of any pair of sequences to differ per base pair?

This is more straightforward: the alignable portion of the human genome is expected to show approximately 0.1% differences. However, this is pretty much only counting SNVs. This will vary from species to species. Off the top of my head, I remember that interfertile Arabidopsis thaliana strains can differ by anything from 0.1% to 1% per aligned base.

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