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Re-curate *K. grimontii* reference set + re-run engine (drop misclassified K. pasteurii) #3

Description

@happykhan

The Klebsiella oxytoca complex group (2026-05 expert feedback survey) found that the K. grimontii reference dataset includes ~45 K. pasteurii genomes misclassified as K. grimontii in the high-quality set, plus ~5 more in filtered_out. K. pasteurii is closely related taxonomically so the misclassification is subtle, but it pulls the K. grimontii threshold distribution.

Acceptance:

  • Get the misclassified-accession list from the KO complex group.
  • Remove those genomes from the K. grimontii input set.
  • Re-run qualibact-engine; import via scripts/import_engine_output.py.
  • Remove the "K. pasteurii misclassification" entry from content/species-notes.yml once landed.
  • Spot-check: K. grimontii GC / genome-size distributions should tighten visibly relative to the pre-cleanup engine output.

Survey provenance: see OUTREACH-v1.1.md for the KO complex group's contact info.

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