Files

• Island synteny viewer
• Assembly quality QC
• frequency_table (tsv.gz)
• clade_assignments (tsv.gz)
• strain_inventory (tsv.gz)
• significant_islands (tsv.gz)
• island_pfam_enrichment (tsv.gz)
• pangenome_openness (tsv.gz)
• per_strain_summary (tsv.gz)
• classification_counts (tsv.gz)
• island_size_distribution (tsv.gz)
• marker_summary (tsv.gz)
• islands_with_domains (tsv.gz)
• assembly_quality_vs_content (tsv.gz)
• assembly_quality_correlations (tsv.gz)
• diagnostics (tsv.gz)
• group_class_overlap (tsv.gz)

Pipeline diagnostics

• rescue_redundancy [TRIGGERED]: 15183898/19580657 (77.5%) 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 [TRIGGERED]: max |rho| = 0.44 (rho = -0.4363, accessory_present vs n50 (partial, controlling total_length), n = 169 strains); threshold 0.3. See assembly_quality_report.md (issue #130). Between-strain accessory-content comparisons are confounded by assembly fragmentation on this dataset.
  • prune option: exclude or flag the most fragmented assemblies (highest n_contigs in assembly_quality_vs_content.tsv) and rerun
  • prune option: report accessory-content comparisons with assembly quality as a covariate, not as raw per-strain counts
• 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.

Pangenome Island + Pfam Enrichment Report

Pangenome composition

Ingroup (26051 gene families)

• core: 6836 (26.2%)
• soft_core: 609 (2.3%)
• shell: 4012 (15.4%)
• cloud: 6786 (26.0%)
• singleton: 7808 (30.0%)

Not counted in this group's classes:

• nonrep_only: 1398
• outgroup_only: 20296

Outgroup (32571 gene families)

• core: 6363 (19.5%)
• soft_core: 637 (2.0%)
• shell: 4621 (14.2%)
• cloud: 11866 (36.4%)
• singleton: 9084 (27.9%)

Not counted in this group's classes:

• nonrep_only: 3587
• ingroup_only: 11587

Pangenome openness

Heaps' law fit: κ=9013.9, γ=0.263 (R²=0.997) -- pangenome is open (γ < 1).

Extrapolated asymptotic core-genome size: 293 families.

Per-strain summary

Families per strain: min=8961, median=9583, max=10330 (n=529 strains). See per_strain_summary.tsv for outliers.

Outlier strains (singleton-count modified z-score beyond threshold): B3476, h5384, CA14, 485B-1_L_OLD_CPA0023, 4545-MICE, GT-101, UTAH_23742X6, FMC778, GT-129, GT-139, VFC084_CPA0067, GT-123, GT-160, GT-133, SOIL_604-1_L_OLD_CPA066, B11863, Michoacan_2, VFC083, CA1, GT-100, B11002, Cocci_1400035797, UTAH_20380X2, COCPO_34698, COCSP-3505, B14286, COCPO_195881, B11518, NACVFR_4542, SA14, GT-147, COCPO_4545, NACVFR_2566, 730333_Guatemala, B0858-Guatemala, 730332_Guatemala, 409B-0_L_OLD_CPA0011, UTAH_9443

Ingroup vs outgroup content

Each gene family's class in the ingroup against its class in the outgroup (counts; colour is log-scaled).

Families in both groups, split by ingroup class, and families found in one group only.

Every non-empty group-class combination, largest first.

Counts: the run's group_class_overlap.tsv table.

Accessory islands

12197 statistically significant accessory islands found (built from adjacency of non-core genes, gated by containing at least one FDR-significant physically-linked pair).

Top islands (by size):

7873 single-strain islands excluded (present in one strain only -- strain-private content, which dominates the size ranking).

Pair classification breakdown

• trans_unconfirmed: 67648
• unexplained_physical: 5014
• ambiguous_linkage: 1985
• insufficient_data: 1202

Pfam domain enrichment