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In a discussion of the mutations S:Q677H and S:Q677P in SARS-CoV-2 it was mentioned that the mutations leading to this result are "against the tendency" of preferred mutations on the nucleotide level. It was also stated as a well known fact, that the rate of mutations depends on the original and mutated base.

So I'd like to know the mutations rates for all possible base pairs in Human Coronaviruses, or a pointer to reference where I can look them up. A less specific but still applicable reference is also welcome, as well as relative mutation frequencies given in some arbitrary units.

EDIT in response to comment by @David: This is the relevant part of a preprint by Hodcroft et al. on the top of page 5

The amino acid Q changes to H due to a mutation at nucleotide position 23593. Notably, in four of these six lineages, the mutation changes from G to U, whereas in the other two, it changes from G to C (FIG 2B). In contrast, the S:Q677P variant occurs by virtue of an A to C change at position 23592. All mutations leading to Q677H or Q677P involve transversions. Hence, their spontaneous occurrence is generally disfavored relative to transitions. In SARS-CoV-2 samples from human infections, A to C and G to C transversions occur at only ~10% the frequency of C to U transitions, while G to U mutations are more common, occurring half as frequently as C to U. (Wright, Lakdawala and Cooper, 2020) (Ratcliff and Simmonds, 2021).

EDIT 2: Learning more about the terminology, I am looking for a Nucleotide Substitution Model or a Mutation Profile in the described environment, especially in a best fit of the empirical data.

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    $\begingroup$ Please provide a reference for your assertions, and explain what you mean by source and target base, as the terms are unfamiliar, at least to me. Also let us know the results of your own attempts to answer this question. $\endgroup$
    – David
    Commented Feb 21, 2021 at 8:31
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    $\begingroup$ The sun is shining for a change, and am going out for a walk, but it looks like a reference to a general difference in frequency of transitions and transversions, which has a straightforward structural basis. There may already be an answer on this topic here, but if not and nobody else does, I’ll post later. $\endgroup$
    – David
    Commented Feb 21, 2021 at 13:45
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    $\begingroup$ Here is an answer to a question about transitions and transversions. Do you understand how the different in overall frequency of these types of mutations is a general thing and has nothing to do with the gene, in the first instance? If this answers your question, I would delete it. If not, explain what more you wish to know. But in any case remove the terms "source" and "target" — they are non-standard and IMHO badly chosen. "Original" base and "mutated" base is clear and unambiguous. $\endgroup$
    – David
    Commented Feb 21, 2021 at 18:11
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    $\begingroup$ The linked question is a good resource, thank you for finding that one, but it does not go down to a quantitative level. I am interested in mutation rates occurring in the wild, not under some mutagene agents. $\endgroup$
    – Sir Cornflakes
    Commented Feb 21, 2021 at 18:36
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    $\begingroup$ The general knowledge about transitions and transversions IS based on observations in what you term "the wild", as is knowledge about, for example, the greater mutation rate of RNA viruses. The details of the mechanisms that explain these observations is necessary for a rational scientific understanding of them. I suspect that you were unaware of this, in which case I think you would be better advised to do some serious reading in this area rather than responding with vague statements about "being interested in mutation rates occurring in the wild". And "target mutation" still doesn't work. $\endgroup$
    – David
    Commented Feb 21, 2021 at 20:55

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I finally found a paper with numbers, it is Host-directed editing of the SARS-CoV-2 genome by Tobias Mourier, Mukhtar Sadykov, Michael J.Carr, Gabriel Gonzale, William W. Hall, and Arnab Pain.

The authors give relative numbers in percent, so all mutations make up 100%. C>U is by far the most frequent one, making up 36.9% of all mutations, followed by G>U 17.6%, U>C 12.6%, A>G 10.9%, and G>A 10.6%. The rest are much rarer: C>A 2.6%, A>U 2.4%, A>C 1.6%, G>C 1.6%, U>G 1.5%, U>A 1.4%, and finally the rarest one, C>G 0.3%.

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  • $\begingroup$ are dna mutations random in the quantum mechanical 'unknowable' sense, or are transcription errors determined in the dark by what molecules happen to be close by, ph-levels, etc during dna replication? $\endgroup$
    – user69150
    Commented Feb 1, 2022 at 15:44
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    $\begingroup$ This one is specific to RNA mutations, and the article cited suggests some mechanisms responsible for the differences in the rates. Also read the comments below the question about transitions and transversions, in general transitions are more probable than transversions. $\endgroup$
    – Sir Cornflakes
    Commented Feb 1, 2022 at 16:22

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