rescue_redundancy [TRIGGERED]: 8811089/10030379 (87.8%) rescuable cells overlap a predicted gene already assigned to a different family in that strain -- the same locus double-counted, not a genuine annotation dropout (issue #133).
prune option: do not enable rescue (--pangenome_rescue_enable false); see clustering sweep #132 before re-enabling
prune option: verify --pangenome_rescue_structural_filter is enabled (default true) -- it is the mechanism that removes these cells, not merely detects them
assembly_quality_confound [OK]: max |rho| = 0.08 (rho = 0.0789, accessory_present vs n50 (raw), n = 293 strains); threshold 0.3. See assembly_quality_report.md (issue #130).
clade_structure_validity [not computed]: trips when: PCoA1 variance share < ~50%, split-half ARI < 0.8, or between/within clade distance ratio < ~2. Not yet computed by this pipeline -- see #131.
gain_loss_skew [not computed]: trips when: gain:loss ratio > 20:1 or ambiguous-polarity fraction < 2%. Not yet computed by this pipeline -- see issue #134's calibration reference.
Synteny (clinker)
Accessory island synteny
Islands shown
Located islands (total)
Excluded
Truncated
Strains
Select an island from the list to view its synteny grid.
