Files
- Island synteny viewer
- Locus summary
- Starships, islands and SM clusters
- 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)
Pipeline diagnostics
- 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.
Pangenome report
Definitions
- Gene family: a cluster of proteins from all strains at the tier-1 clustering identity and coverage. A family is present in a strain when a member protein is annotated there, or (with rescue on) when a TBLASTN hit marks it
genome_only. - Frequency class (computed separately for each group, over that group's representative strains):
singleton= one representative strain; otherwise by the fraction of representatives:core>= 0.95,soft_core>= 0.90,shell>= 0.15,cloudbelow 0.15 (defaults; the run parameters set them). A family in no representative getsnonrep_only(only in near-identical strains that were dereplicated away),outgroup_onlyoringroup_only(only in the other group), orabsent. - Representative strain: one strain kept per group of near-identical strains (Mash dereplication). Counts of "strains" that include non-representatives are said so.
- Accessory island: a run of consecutive non-core genes in one strain that contains at least one significantly co-occurring pair that is also physically linked. The islands are not tested as units.
Pangenome composition
Ingroup (36302 gene families)
- core: 7165 (19.7%)
- soft_core: 667 (1.8%)
- shell: 4612 (12.7%)
- cloud: 10561 (29.1%)
- singleton: 13297 (36.6%)
Not counted in this group's classes:
- nonrep_only: 5814
- outgroup_only: 5838
Pangenome openness
Heaps' law fit: κ=7492.1, γ=0.317 (R²=0.980) -- pangenome is open (γ > 0; γ = 1 would mean every new strain adds the same number of new families). The curve counts every strain in the presence matrix, including near-identical strains and the outgroup.
Extrapolated asymptotic core-genome size: 2423 families.
Per-strain summary
Families per strain: min=9525, median=10365, max=11911 (n=295 strains). See per_strain_summary.tsv for outliers.
Outlier strains (singleton-count modified z-score beyond threshold): Asfu_UD1, Asfu_CNMCM8686, Asfu_niveus, Asfu_AfB7, Asfu_AfB8, Asfu_AfB6, Asfu_E1202, Asfu_Z5, Asfu_NRZ2016063, Asfu_B171L1, Asfu_L2241, Asfu_D223L5, Asfu_AfB2, Asfu_I1493, Asfu_NRZ2017534, Asfu_E175s2, Asfu_A1163, Asfu_B5233, Asfu_C172L1, Asfu_AF1009B, Asfu_ATCC_42202, Asfu_eAF1436, Asfu_eAF1023, Asfu_08190230, Asfu_H237, Asfu_W72310, Asfu_Af293, Asfu_eAF1090, Asfu_ATCC_46645, Asfu_H1106
The outgroup has too few representative genomes to bin on its own; outgroup genomes use ingroup classes.
Ingroup vs outgroup content
Not shown: the outgroup is not binned (too few representative genomes).
Accessory islands
11676 accessory islands found (built from adjacency of non-core genes, gated by containing at least one FDR-significant physically-linked pair). The islands themselves are not tested as units.
Top islands (by size):
6758 single-strain islands excluded (present in one strain only -- strain-private content, which dominates the size ranking).
Pair classification breakdown
- trans_unconfirmed: 616750
- trans: 543757
- insufficient_data: 188361
- unexplained_physical: 10264
- ambiguous_linkage: 4441
Trans-module genomic clustering
Scale: same contig, at least 11 genes apart, gene starts within max 100 kb. Null: accessory genes of the same strain, 200 permutations, seed 0. Pairs on different contigs are excluded, not counted as distant. With millions of pairs a tiny effect still reaches the smallest possible p, so read the effect ratio first.
| Module | Families | Strains | Obs. frac (same contig) | Null | Effect | p | Effect (all pairs) | p (all pairs) | Cross-contig excluded |
|---|---|---|---|---|---|---|---|---|---|
| 0 | 2767 | 295 | 0.256 | 0.245 | 1.05 | 0.005 | 1.10 | 0.005 | 98.9% |
| 1 | 2188 | 295 | 0.342 | 0.245 | 1.40 | 0.005 | 1.63 | 0.005 | 98.3% |
| 10 | 2 | 15 | - | 0.667 | - | - | 0.00 | 1.000 | 100.0% |
| 11 | 2 | 9 | - | 0.750 | - | - | 0.00 | 1.000 | 100.0% |
| 12 | 2 | 7 | - | 0.500 | - | - | 0.00 | 1.000 | 100.0% |
| 2 | 1512 | 295 | 0.050 | 0.051 | 0.97 | 1.000 | 1.00 | 0.647 | 90.3% |
| 3 | 902 | 295 | 0.162 | 0.171 | 0.95 | 1.000 | 1.10 | 0.005 | 98.1% |
| 4 | 579 | 295 | 0.469 | 0.441 | 1.06 | 0.005 | 1.27 | 0.005 | 99.3% |
| 5 | 145 | 178 | 0.515 | 0.181 | 2.85 | 0.005 | 12.64 | 0.005 | 86.5% |
| 6 | 122 | 181 | 0.077 | 0.047 | 1.65 | 0.005 | 1.57 | 0.005 | 89.6% |
| 7 | 8 | 9 | 1.000 | 0.115 | 8.70 | 0.005 | 50.43 | 0.005 | 28.7% |
| 8 | 4 | 22 | 0.000 | 0.112 | 0.00 | 1.000 | 0.00 | 1.000 | 42.9% |
| 9 | 3 | 8 | - | 0.051 | - | - | 0.00 | 1.000 | 100.0% |
Pfam domain enrichment
| Domain | Fisher p | FDR q |
|---|---|---|
| APH | 6.69e-14 | 1.32e-10 |
| DUF3435 | 3.80e-13 | 3.76e-10 |
| DDE_1 | 6.15e-11 | 3.54e-08 |
| GloB_C | 7.16e-11 | 3.54e-08 |
| DUF3723 | 8.16e-09 | 3.23e-06 |
| HSF_DNA-bind | 1.66e-07 | 5.46e-05 |
| RVT_1 | 2.80e-07 | 7.92e-05 |
| HAC6_helical | 3.79e-07 | 8.76e-05 |
| DUF3723_N | 3.99e-07 | 8.76e-05 |
| Glyco_hydro_18 | 1.71e-06 | 3.37e-04 |
| HAC6_N | 4.52e-06 | 8.12e-04 |
| HTH_Tnp_Tc5 | 1.71e-05 | 2.82e-03 |
| Glyco_hydro_71 | 4.17e-05 | 6.34e-03 |
| Acyl_transf_1 | 4.52e-05 | 6.38e-03 |
| HNH_2 | 4.94e-05 | 6.50e-03 |
| Glyco_hydro_99 | 1.24e-04 | 1.53e-02 |
| LysM4_N | 1.63e-04 | 1.90e-02 |
| Exo_endo_phos_2 | 2.36e-04 | 2.59e-02 |
| AFUB_07903_YDR124W_hel | 3.46e-04 | 3.60e-02 |
| DUF2293 | 4.48e-04 | 4.43e-02 |
| DUF6736 | 5.28e-04 | 4.98e-02 |