Private mutations

General
1

Good morning,

we are analyzing SARS-Cov-2 sequencing data with NextClade and for all sequences (384 samples per run) we obtain a bad quality score concerning the flag “Private mutations”.
How would you explain this fact? Have you ever find a similar issue? Are the sequences good enough to be submitted to public databases?

Thank you and best regards
Anna

2

Hi Anna,
private mutations are differences to the nearest node in the reference tree. These are further split up into reversions, labeled mutations, and others. A bad score in the private mutation category could mean one of the following:

  • good sequences that with out representation in the reference tree.
  • good sequences that are recombinant genomes not yet designated by Pango
  • bad sequence that are are contaminated with another variant or the reference.

which of the three needs to be determined by manual inspection.

Here is some additional information:
https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/07-quality-control.html

best regards,
richard

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