Private mutations

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

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