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)
• group_class_overlap (tsv.gz)

Pipeline diagnostics

• rescue_redundancy [TRIGGERED]: 15128104/19521312 (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 = -0.4404, 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 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, cloud below 0.15 (defaults; the run parameters set them). A family in no representative gets nonrep_only (only in near-identical strains that were dereplicated away), outgroup_only or ingroup_only (only in the other group), or absent.
• 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 (26047 gene families)

• core: 6846 (26.3%)
• soft_core: 610 (2.3%)
• shell: 4025 (15.5%)
• cloud: 6764 (26.0%)
• singleton: 7802 (30.0%)

Not counted in this group's classes:

• nonrep_only: 1406
• outgroup_only: 20327

Outgroup (32609 gene families)

• core: 6357 (19.5%)
• soft_core: 636 (2.0%)
• shell: 4628 (14.2%)
• cloud: 11894 (36.5%)
• singleton: 9094 (27.9%)

Not counted in this group's classes:

• nonrep_only: 3591
• ingroup_only: 11580

Pangenome openness

Heaps' law fit: κ=9019.9, γ=0.263 (R²=0.997) -- 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: 295 families.

Per-strain summary

Families per strain: min=8972, median=9586, max=10324 (n=529 strains). See per_strain_summary.tsv for outliers.

Outlier strains (singleton-count modified z-score beyond threshold): B3476, h5384, 485B-1_L_OLD_CPA0023, 4545-MICE, CA14, GT-101, UTAH_23742X6, FMC778, GT-129, GT-139, VFC084_CPA0067, GT-160, SOIL_604-1_L_OLD_CPA066, GT-133, B11863, Michoacan_2, VFC083, GT-100, CA1, J_TORRES, B11002, Cocci_1400035797, UTAH_20380X2, COCPO_34698, COCSP-3505, COCPO_195881, SA14, NACVFR_4542, B14286, B11518, GT-147, COCPO_4545, NACVFR_2566, B1249_Guatemala, 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

11968 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):

7733 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
UTAH_23742X163:scaffold_153:1680-58643	31	57.0	2	ABC_membrane, ABC_tran, APH, Chromo, DUF3435, DUF7924, Glyco_tranf_2_3, Glycos_transf_2, Laminin_I, Patatin, Pkinase, Pkinase_fungal, RsgA_GTPase, SPOK2_N, Shootin
Phoenix_9:scaffold_91:32815-71578	24	38.8	2	Chitin_bind_1, DUF7582, FAD_binding_8, Glyco_hydro_18, Kdo, Myb_DNA-bind_5, NAD_binding_6, PK_Tyr_Ser-Thr, Patatin, Pkinase, SMC_N
B0858-Guatemala:scaffold_7:31524-71402	21	39.9	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
COCPO_185672:scaffold_58:31148-71167	21	40.0	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
B16536:scaffold_155:4801-50073	20	45.3	2	EST1_DNA_bind, PhyH
SDVA42:scaffold_36:31416-69708	20	38.3	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
Tucson_3:scaffold_87:39176-79068	20	39.9	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
407-0_S_OLD_CPA0002:scaffold_36:130365-168659	19	38.3	4	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
578-1_L_NEW_CPA0049_alt:scaffold_189:24-32783	19	32.8	2	AFUB_07903_YDR124W_hel, APH, FKBP_C, Kdo, Mis12, PhyH, SPOK2_N
B10917:scaffold_11:31484-73024	19	41.5	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
B3290:scaffold_11:145443-184017	19	38.6	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
J_TORRES:scaffold_20:48568-88530	19	40.0	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
SDVA16:scaffold_6:226520-264896	19	38.4	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
407-1_S_OLD_CPA0004:scaffold_53:38227-76549	18	38.3	7	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
B3326:scaffold_2:583128-621702	18	38.6	2	APH, BTB, HAC6_N, HAC6_helical, HrmA, PK_Tyr_Ser-Thr, Pkinase, RING_XB3-XBAT31, zf-RING_2, zf-RING_UBOX
GT-136:scaffold_132:3810-46411	17	42.6	6	APH, Abhydrolase_3, BD-FAE, Beta-lactamase, COesterase, Fung_rhodopsin, GGACT, HET, PK_Tyr_Ser-Thr, Pkinase
GT-102:scaffold_232:355-29376	17	29.0	2	AFUB_07903_YDR124W_hel, APH, FKBP_C, Kdo, PhyH, SPOK2_N
GT-126:scaffold_179:8071-41691	17	33.6	2	DUF3723, Myb_DNA-bind_6, NAD_binding_6
574-0_S_OLD_CPA0039:scaffold_8:318724-336174	16	17.4	7	APH, DASH_Hsk3, DUF7924, Kinase-like, PK_Tyr_Ser-Thr, Pkinase
B12526:scaffold_35:142210-164021	16	21.8	4	ACP_SdgA_C, ADH_N, APH, Choline_kinase, KR, MFS_1, Methyltransf_12, Methyltransf_23, PP-binding, PS-DH, PhyH, Sugar_tr, TRI12, adh_short, adh_short_C2

Pair classification breakdown

• trans: 65147
• unexplained_physical: 5048
• trans_unconfirmed: 3316
• ambiguous_linkage: 2009
• insufficient_data: 1539

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	679	529	0.407	0.518	0.79	1.000	0.55	1.000	99.7%
1	643	529	0.381	0.409	0.93	1.000	0.95	1.000	99.1%
10	151	529	0.731	0.411	1.78	0.005	21.29	0.005	80.9%
100	2	56	-	0.419	-	-	0.00	1.000	100.0%
101	2	117	-	0.450	-	-	0.00	1.000	100.0%
102	2	7	-	1.000	-	-	0.00	1.000	100.0%
103	2	13	-	0.476	-	-	0.00	1.000	100.0%
105	2	38	-	0.310	-	-	0.00	1.000	100.0%
107	2	5	-	0.333	-	-	0.00	1.000	100.0%
108	2	8	-	0.333	-	-	0.00	1.000	100.0%
11	72	529	0.535	0.423	1.26	0.010	2.91	0.005	87.4%
111	2	13	-	0.267	-	-	0.00	1.000	100.0%
112	2	16	-	0.480	-	-	0.00	1.000	100.0%
114	2	9	-	0.273	-	-	0.00	1.000	100.0%
115	2	5	-	0.500	-	-	0.00	1.000	100.0%
116	2	17	-	0.333	-	-	0.00	1.000	100.0%
117	2	7	-	0.750	-	-	0.00	1.000	100.0%
118	2	5	-	0.000	-	-	-	1.000	100.0%
119	2	9	-	0.375	-	-	0.00	1.000	100.0%
12	52	457	0.887	0.419	2.12	0.005	77.98	0.005	46.4%
120	2	15	-	0.364	-	-	0.00	1.000	100.0%
121	2	6	-	0.375	-	-	0.00	1.000	100.0%
122	2	8	-	0.667	-	-	0.00	1.000	100.0%
123	2	6	-	0.500	-	-	0.00	1.000	100.0%
124	2	6	-	0.667	-	-	0.00	1.000	100.0%
125	2	6	-	0.222	-	-	0.00	1.000	100.0%
126	2	11	1.000	0.500	2.00	0.533	114.29	0.005	63.6%
127	2	9	-	0.667	-	-	0.00	1.000	100.0%
128	2	7	-	0.333	-	-	0.00	1.000	100.0%
13	45	506	0.333	0.411	0.81	0.866	0.43	0.995	97.6%
130	2	8	-	0.200	-	-	0.00	1.000	100.0%
131	2	1	-	-	-	-	-	1.000	100.0%
132	2	7	-	0.500	-	-	0.00	1.000	100.0%
133	2	3	-	1.000	-	-	0.00	1.000	100.0%
135	2	2	-	1.000	-	-	0.00	1.000	100.0%
136	2	3	-	0.200	-	-	0.00	1.000	100.0%
139	2	6	-	0.500	-	-	0.00	1.000	100.0%
14	35	90	0.526	0.400	1.31	0.070	7.41	0.005	53.9%
140	2	7	-	0.500	-	-	0.00	1.000	100.0%
141	2	7	-	0.600	-	-	0.00	1.000	100.0%
142	2	22	-	0.333	-	-	0.00	1.000	100.0%
146	2	186	0.000	0.462	0.00	1.000	0.00	1.000	99.5%
147	2	9	-	0.545	-	-	0.00	1.000	100.0%
15	15	323	0.521	0.444	1.17	0.289	18.35	0.005	41.7%
151	2	22	-	0.154	-	-	0.00	1.000	100.0%
153	2	1	-	0.250	-	-	0.00	1.000	100.0%
154	2	7	-	0.625	-	-	0.00	1.000	100.0%
155	2	1	-	0.500	-	-	0.00	1.000	100.0%
157	2	6	-	1.000	-	-	0.00	1.000	100.0%
16	7	27	1.000	0.435	2.30	0.323	92.63	0.005	55.6%
161	2	71	-	0.407	-	-	0.00	1.000	100.0%
162	2	6	-	0.222	-	-	0.00	1.000	100.0%
163	2	45	1.000	0.402	2.49	0.371	437.50	0.005	22.2%
164	2	36	-	0.543	-	-	0.00	1.000	97.2%
165	2	17	-	0.556	-	-	0.00	1.000	100.0%
166	2	1	-	-	-	-	-	1.000	100.0%
167	2	2	-	-	-	-	-	1.000	100.0%
168	2	5	-	0.667	-	-	0.00	1.000	100.0%
169	2	242	-	0.480	-	-	0.00	1.000	100.0%
17	7	395	0.000	0.420	0.00	1.000	0.00	1.000	60.1%
170	2	5	-	0.286	-	-	0.00	1.000	100.0%
172	2	15	-	0.688	-	-	0.00	1.000	100.0%
173	2	6	-	0.600	-	-	0.00	1.000	100.0%
174	2	6	1.000	0.750	1.33	0.800	66.67	0.020	83.3%
175	2	11	-	0.714	-	-	0.00	1.000	100.0%
176	2	3	-	0.800	-	-	0.00	1.000	100.0%
179	2	6	-	0.500	-	-	0.00	1.000	100.0%
18	6	83	1.000	0.473	2.11	0.238	141.76	0.005	47.7%
180	2	10	-	0.833	-	-	0.00	1.000	100.0%
181	2	11	1.000	0.250	4.00	0.294	250.00	0.005	54.5%
182	2	10	-	0.200	-	-	0.00	1.000	100.0%
183	2	12	-	0.333	-	-	0.00	1.000	100.0%
184	2	9	-	0.531	-	-	0.00	1.000	100.0%
186	2	10	-	0.000	-	-	-	1.000	100.0%
187	2	8	-	0.438	-	-	0.00	1.000	100.0%
188	2	9	-	0.364	-	-	0.00	1.000	100.0%
189	2	10	-	0.429	-	-	0.00	1.000	100.0%
19	5	451	0.984	0.397	2.48	0.055	69.32	0.005	82.1%
190	2	13	-	0.267	-	-	0.00	1.000	100.0%
2	456	529	0.620	0.436	1.42	0.005	2.66	0.005	97.9%
20	5	1	-	1.000	-	-	0.00	1.000	100.0%
21	5	36	-	0.464	-	-	0.00	1.000	70.9%
22	5	94	-	0.430	-	-	0.00	1.000	100.0%
23	4	17	-	0.460	-	-	0.00	1.000	100.0%
24	4	27	-	0.554	-	-	0.00	1.000	38.5%
25	4	30	-	0.462	-	-	0.00	1.000	54.7%
26	4	472	0.000	0.405	0.00	1.000	0.00	1.000	92.6%
27	4	489	0.032	0.420	0.08	0.970	0.31	0.851	97.6%
28	4	56	-	0.393	-	-	0.00	1.000	100.0%
29	4	38	1.000	0.487	2.06	0.429	58.88	0.005	81.4%
3	427	529	0.702	0.429	1.64	0.005	2.76	0.005	97.6%
30	4	5	-	0.500	-	-	0.00	1.000	100.0%
31	4	8	-	0.250	-	-	0.00	1.000	100.0%
32	4	36	-	0.415	-	-	0.00	1.000	100.0%
33	4	3	-	0.375	-	-	0.00	1.000	100.0%
34	3	35	-	0.544	-	-	0.00	1.000	58.8%
35	3	433	0.000	0.429	0.00	1.000	0.00	1.000	99.7%
36	3	99	-	0.398	-	-	0.00	1.000	100.0%
37	3	13	-	0.600	-	-	0.00	1.000	100.0%
38	3	381	0.000	0.416	0.00	1.000	0.00	1.000	99.8%
39	3	6	-	0.429	-	-	0.00	1.000	100.0%
4	350	529	0.375	0.464	0.81	1.000	0.96	0.841	99.4%
40	3	10	-	0.370	-	-	0.00	1.000	66.7%
41	3	18	0.167	0.386	0.43	0.435	22.22	0.050	66.7%
42	3	12	-	0.375	-	-	0.00	1.000	100.0%
43	3	18	-	0.579	-	-	0.00	1.000	100.0%
44	3	28	-	0.310	-	-	0.00	1.000	100.0%
45	3	24	-	0.429	-	-	0.00	1.000	100.0%
46	3	300	0.957	0.437	2.19	0.182	22.56	0.005	94.7%
47	3	88	-	0.483	-	-	0.00	1.000	100.0%
48	3	23	-	0.297	-	-	0.00	1.000	100.0%
49	3	60	-	0.368	-	-	0.00	1.000	100.0%
5	240	529	0.936	0.423	2.21	0.005	13.89	0.005	89.8%
50	3	2	-	0.000	-	-	-	1.000	100.0%
52	3	436	1.000	0.433	2.31	0.134	248.41	0.005	28.2%
53	3	5	-	0.333	-	-	0.00	1.000	100.0%
55	3	28	-	0.429	-	-	0.00	1.000	100.0%
57	3	42	-	0.427	-	-	0.00	1.000	100.0%
58	3	54	1.000	0.471	2.12	0.462	280.00	0.005	35.2%
59	3	34	-	0.474	-	-	0.00	1.000	100.0%
6	215	529	0.482	0.424	1.14	0.005	1.39	0.005	99.0%
60	3	12	-	0.556	-	-	0.00	1.000	100.0%
61	3	81	-	0.442	-	-	0.00	1.000	100.0%
62	3	9	-	0.278	-	-	0.00	1.000	100.0%
63	3	7	-	0.643	-	-	0.00	1.000	100.0%
64	3	45	-	0.463	-	-	0.00	1.000	100.0%
65	3	23	-	0.417	-	-	0.00	1.000	100.0%
66	3	446	0.994	0.403	2.46	0.010	99.28	0.005	40.5%
67	3	89	-	0.459	-	-	0.00	1.000	57.5%
68	3	5	-	0.500	-	-	0.00	1.000	100.0%
69	3	1	-	1.000	-	-	0.00	1.000	100.0%
7	212	529	0.721	0.433	1.66	0.005	3.82	0.005	96.0%
70	2	9	-	0.600	-	-	0.00	1.000	100.0%
71	2	41	-	0.446	-	-	0.00	1.000	100.0%
72	2	1	-	-	-	-	-	1.000	100.0%
73	2	74	-	0.409	-	-	0.00	1.000	100.0%
75	2	66	-	0.380	-	-	0.00	1.000	100.0%
76	2	9	-	0.167	-	-	0.00	1.000	100.0%
77	2	56	0.000	0.352	0.00	1.000	0.00	1.000	96.4%
78	2	80	1.000	0.477	2.10	0.470	282.35	0.005	40.0%
79	2	109	0.000	0.387	0.00	1.000	0.00	1.000	99.1%
8	190	529	0.509	0.424	1.20	0.005	1.87	0.005	98.1%
80	2	10	-	0.556	-	-	0.00	1.000	100.0%
81	2	79	1.000	0.401	2.49	0.333	390.00	0.005	1.3%
82	2	17	1.000	0.406	2.46	0.412	428.57	0.005	11.8%
83	2	36	1.000	0.378	2.65	0.387	516.67	0.005	13.9%
84	2	143	1.000	0.415	2.41	0.346	2.96	0.090	6.9%
85	2	8	-	0.538	-	-	0.00	1.000	100.0%
86	2	112	-	0.277	-	-	0.00	1.000	100.0%
87	2	26	-	0.259	-	-	0.00	1.000	100.0%
88	2	40	1.000	0.347	2.88	0.324	571.43	0.005	0.0%
89	2	130	-	0.351	-	-	0.00	1.000	100.0%
9	172	529	0.423	0.429	0.99	0.692	1.00	0.433	99.1%
90	2	6	-	0.455	-	-	0.00	1.000	100.0%
91	2	35	-	0.636	-	-	0.00	1.000	100.0%
92	2	5	-	0.318	-	-	0.00	1.000	100.0%
93	2	66	1.000	0.350	2.86	0.341	87.50	0.005	89.4%
94	2	228	1.000	0.470	2.13	0.314	1.65	0.502	99.6%
95	2	109	-	0.447	-	-	0.00	1.000	100.0%
97	2	1	-	0.000	-	-	-	1.000	100.0%
98	2	118	-	0.420	-	-	0.00	1.000	100.0%
99	2	83	-	0.432	-	-	0.00	1.000	100.0%

Pfam domain enrichment

Domain	Fisher p	FDR q
DUF3435	5.09e-18	4.73e-15
DUF3723	3.26e-12	1.51e-09
APH	1.86e-09	5.75e-07
Pkinase_fungal	7.88e-08	1.83e-05
Pkinase	1.58e-06	2.84e-04
DUF3723_N	1.84e-06	2.84e-04
DUF7924	2.42e-06	3.20e-04
NAD_binding_6	1.66e-05	1.93e-03
DUF7779	7.22e-05	7.44e-03
ABC_tran	2.94e-04	2.73e-02
Myb_DNA-bind_6	5.60e-04	4.69e-02
p450	6.06e-04	4.69e-02