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)
Pipeline diagnostics
- rescue_redundancy [TRIGGERED]: 13595397/15613082 (87.1%) 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| = 0.65 (rho = 0.6461, accessory_present vs n50 (raw), n = 344 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 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 (37443 gene families)
- core: 5463 (14.6%)
- soft_core: 616 (1.6%)
- shell: 2525 (6.7%)
- cloud: 12354 (33.0%)
- singleton: 16485 (44.0%)
Not counted in this group's classes:
- nonrep_only: 2881
- outgroup_only: 14472
Pangenome openness
Heaps' law fit: κ=4602.1, γ=0.426 (R²=0.982) -- 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: 1 families.
Per-strain summary
Families per strain: min=6901, median=7659, max=12309 (n=346 strains). See per_strain_summary.tsv for outliers.
Outlier strains (singleton-count modified z-score beyond threshold): Bd_CJB4, Bd_TST75, Bd_ETH2_ET, Bd_CJB5-2, Bd_CJB7, Bd_JEL627, Bd_JEL359, Bd_CLFT023, Bd_Sample_55899, Bd_KBO_327, Bd_ACON_CH, Bd_KRBOOR_331, Bd_KRBOOR_317, Bd_KRBOOR_323, Bd_KB347, Bd_Sample_55926, Bd_SA-EC5, Bd_Sample_55945, Bd_Sample_55940, Bd_Sample_55928, Bd_Sample_55922, Bd_DB8-4, Bd_Sample_55918, Bd_Sample_55925, Bd_Sample_55929, Bd_CLFT026, Bd_Sample_55917, Bd_Sample_55936, Bd_CLFT144, Bd_TER_4.2, Bd_Sample_55931, Bd_Sample_55914, Bd_STR3_CH, Bd_JEL427-P17, Bd_40.OZ, Bd_RTP6, Bd_AP15_IT, Bd_JEL427-P39
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
19087 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):
15472 single-strain islands excluded (present in one strain only -- strain-private content, which dominates the size ranking).
| Locus (strain:contig:start-end) | Genes in island (#) | Span (kb) | Strains (#) | Pfam domains |
|---|---|---|---|---|
| Bd_KB23:scaffold_12:620095-652647 | 22 | 32.6 | 2 | IFT74, Mrr_cat, PDZ_4, Peptidase_S41, RRG7 |
| Bd_IA042_Highly_passaged:scaffold_13:606769-632226 | 19 | 25.5 | 2 | CCDC39, Mrr_cat, RRG7 |
| Bd_IA_12No5:scaffold_17:59225-149831 | 17 | 90.6 | 2 | NADHdh |
| Bd_FG32:scaffold_18:65715-156182 | 16 | 90.5 | 3 | NADHdh |
| Bd_34.OZ:scaffold_18:53734-140314 | 16 | 86.6 | 2 | NADHdh |
| Bd_ANS_13No1:scaffold_17:59753-150386 | 15 | 90.6 | 4 | NADHdh |
| Bd_15.OZ:scaffold_18:58083-148550 | 15 | 90.5 | 2 | NADHdh |
| Bd_33.OZ:scaffold_18:66386-152966 | 15 | 86.6 | 2 | NADHdh |
| Bd_AoCH15_B:scaffold_18:58078-148544 | 15 | 90.5 | 2 | NADHdh |
| Bd_BAV_OBER_3:scaffold_18:49280-139706 | 15 | 90.4 | 2 | NADHdh |
| Bd_34.OZ:scaffold_10:704420-728789 | 12 | 24.4 | 2 | Aa_trans, Asp, TAXi_C |
| Bd_ANS_13No12:scaffold_17:8770-56840 | 12 | 48.1 | 2 | COX1 |
| BdBE6:scaffold_15:414519-432506 | 12 | 18.0 | 2 | Asp, Chromo_shadow, DUF2009, TAXi_C |
| Bd_Aus2:scaffold_17:8202-55791 | 12 | 47.6 | 2 | COX1 |
| Bd_MC58:scaffold_10:706424-727527 | 12 | 21.1 | 2 | Asp, TAXi_C |
| Bd_15.OZ:scaffold_18:8907-55821 | 11 | 46.9 | 6 | COX1 |
| Bd_40.OZ:scaffold_10:705251-728824 | 11 | 23.6 | 3 | Aa_trans, Asp, TAXi_C |
| Bd_42.OZ:scaffold_18:8907-57583 | 11 | 48.7 | 3 | COX1 |
| Bd_09.OZ:scaffold_17:149045-173350 | 11 | 24.3 | 2 | Arm, Asp, F-box, F-box-like, TAXi_C |
| Bd_28.OZ:scaffold_11:709022-733280 | 11 | 24.3 | 2 | Aa_trans, Asp, TAXi_C |
Pair classification breakdown
- trans_unconfirmed: 592684
- trans: 421227
- insufficient_data: 217788
- unexplained_physical: 5237
- ambiguous_linkage: 1913
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 | 3366 | 346 | 0.092 | 0.090 | 1.02 | 0.005 | 1.06 | 0.005 | 92.2% |
| 1 | 2565 | 346 | 0.091 | 0.090 | 1.01 | 0.005 | 1.00 | 0.294 | 92.6% |
| 2 | 1357 | 346 | 0.068 | 0.076 | 0.90 | 1.000 | 1.06 | 0.005 | 89.8% |
| 3 | 3 | 7 | - | 0.108 | - | - | 0.00 | 1.000 | 100.0% |
| 4 | 3 | 12 | - | 0.079 | - | - | 0.00 | 1.000 | 100.0% |
| 5 | 2 | 4 | - | 0.117 | - | - | 0.00 | 1.000 | 100.0% |
Pfam domain enrichment
| Domain | Fisher p | FDR q |
|---|---|---|
| Asp | 7.89e-53 | 1.35e-49 |
| TAXi_C | 1.69e-25 | 1.44e-22 |
| Arm | 2.74e-15 | 1.56e-12 |
| TgMIC1 | 3.38e-14 | 1.44e-11 |
| DUF4246_N | 3.64e-13 | 1.24e-10 |
| Peptidase_S41 | 9.66e-08 | 2.74e-05 |
| DUF4246 | 4.50e-07 | 1.10e-04 |
| Adaptin_N | 1.35e-05 | 2.87e-03 |
| Peptidase_M4_C | 3.33e-05 | 6.31e-03 |
| Cast | 2.06e-04 | 3.51e-02 |