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)
Preview of the island locus view and clinker synteny panel (NovInvenio branch
locus-view-batf8b3b97, PRs stajichlab/NovInvenio#201 and #204, not yet merged) on therescue_freqpol_immitis_in_posadasii_outrun. The DNA-check thresholds (90% identity, 80% coverage), the 20 kb gap split and the 5-95% polymorphism band are unvalidated defaults. Open Island synteny viewer below for the locus view; clinker figures are published for the top 25 loci.
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
| Domain | Fisher p | FDR q |
|---|---|---|
| DUF3435 | 2.25e-17 | 2.13e-14 |
| DUF3723 | 7.77e-11 | 3.68e-08 |
| APH | 2.30e-08 | 7.26e-06 |
| Pkinase_fungal | 6.05e-08 | 1.43e-05 |
| Pkinase | 3.30e-06 | 6.26e-04 |
| DUF7924 | 5.33e-06 | 8.43e-04 |
| NAD_binding_6 | 1.80e-05 | 2.44e-03 |
| DUF3723_N | 4.11e-05 | 4.87e-03 |
| Drf_FH1 | 7.24e-05 | 7.34e-03 |
| DUF7779 | 7.74e-05 | 7.34e-03 |
| p450 | 2.07e-04 | 1.79e-02 |
| ABC_tran | 3.27e-04 | 2.58e-02 |
| DUF676 | 3.97e-04 | 2.90e-02 |
| Myb_DNA-bind_6 | 5.98e-04 | 4.05e-02 |