I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup.

Sometimes I find that there are two consistent variants for the same position, but I can only generate one consensus sequence.

Which variant should I target:

  • The majority variant
  • The minoritarian one if I find that this SNP is under-reported in other public samples?
  • Are both required

What one is best practice?

  • $\begingroup$ Its a fundamental question. It would be useful to understand a little more about your sample $\endgroup$
    – M__
    Commented Feb 26, 2022 at 23:12
  • $\begingroup$ It was long ago... What do you need to know? $\endgroup$
    – juanjo75es
    Commented Feb 28, 2022 at 21:28
  • $\begingroup$ thanks, let me think a lot and I will formulate a question on the site and drop a comment to flag notify you $\endgroup$
    – M__
    Commented Mar 1, 2022 at 15:13

1 Answer 1


Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are:

  1. Use the ancestral allele (this isn't always apparent)
  2. Use the most common allele
  3. Randomly choose

I think 1 and 2 are generally preferred, with 2 being easier to implement.


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