peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Adding a Pythiogeton proliferatum sequence to curated DB #586

Closed peterjc closed 8 months ago

peterjc commented 8 months ago

Follow on from #585.

Adding JQ610197 and JQ610199 (same sequence). We see something just 4bp different (with the assumed 32bp leader) in a collaborator's sample at an accepatable read depth.

Note the right primer GCARRGACTTTCGTCCCYRC match is poor:

       ...CCGAGGACGAAAGTCTTTGG... (apparent match)
          xxxx|||||||||||xx||x
          GYRGGGACGAAAGTCYYTGC    (right primer RC)

We can make no guesses about the left primer binding as the sequences are missing the start.

peterjc commented 8 months ago

The collaborators dataset isn't part of what we're using to automatically update https://github.com/peterjc/thapbi-pict/blob/v1.0.5/database/Oomycota_ITS1_obs.fasta thus adding it to the curated file

The 4bp difference means we'd not automatically import it via Oomycota_ITS1_obs.fasta