Starships, islands and secondary-metabolite clusters
Source: bin/starship_island_overlap.py output for run posadasii_in_immitis_out_v2. A family is 'in an island' when it is a member of >= 1 row of significant_islands.tsv. Background: all non-core families of the run (enrichment.tsv, universe noncore). Exploratory analysis; read the 'Data and limits' box.
| families | islands | islands with >= 2 strains | families in >= 1 island | families in >= 1 multi-strain island |
|---|---|---|---|---|
| 35747 | 16014 | 5825 | 10934 | 5914 |
Starship families in islands
Not available: this run has no Starship element coordinates (summary.tsv has no starship_* metrics). The captain-gene families below are the only Starship proxy.
Captain-gene families (non-core) in islands
Captain gene: tblout targets with full-sequence E <= 1e-05; 6292 hits, 2323 not mapped to a family of this run.
| set | families | in >= 1 island | in >= 1 multi-strain island | islands with >= 1 family of the set | non-core: set families in islands | non-core: all families in islands (background) | fold | hypergeometric p (greater) |
|---|---|---|---|---|---|---|---|---|
| Captain-gene (DUF3435) families | 273 | 211 | 67 | 929 of 16014 | 211 of 270 (0.7815) | 10934 of 28767 (0.3801) | 2.056 | 1.37e-41 |
All universes (enrichment.tsv)
| annotation | universe | N_universe | K_annotated | n_island | k_both | expected_k | fold | odds_ratio | p_hypergeom_greater |
|---|---|---|---|---|---|---|---|---|---|
| captain | cooc_eligible | 10867 | 98 | 7042 | 88 | 63.51 | 1.386 | 4.828 | 1.19e-08 |
| captain | noncore | 28767 | 270 | 10934 | 211 | 102.62 | 2.056 | 5.928 | 1.37e-41 |
Frequency bin and gain/loss direction (class_breakdown.tsv)
| annotation | bin | direction | in_island | n_families |
|---|---|---|---|---|
| captain | cloud | ambiguous | no | 3 |
| captain | cloud | ambiguous | yes | 8 |
| captain | cloud | gain | no | 22 |
| captain | cloud | gain | yes | 114 |
| captain | cloud | loss | no | 1 |
| captain | core | conserved | no | 1 |
| captain | nonrep_only | gain | no | 5 |
| captain | nonrep_only | gain | yes | 8 |
| captain | outgroup_only | absent | no | 7 |
| captain | outgroup_only | absent | yes | 1 |
| captain | shell | ambiguous | no | 2 |
| captain | shell | ambiguous | yes | 4 |
| captain | shell | gain | no | 2 |
| captain | shell | gain | yes | 9 |
| captain | shell | loss | yes | 2 |
| captain | singleton | ambiguous | no | 1 |
| captain | singleton | ambiguous | yes | 1 |
| captain | singleton | gain | no | 16 |
| captain | singleton | gain | yes | 64 |
| captain | soft_core | gain | no | 2 |
Families in islands by annotation set (per element when element coordinates exist).
Secondary-metabolite (SM) clusters
Source: antiSMASH 8.0.1 regions.
Overlap with a Starship: >= 1 gene rule: NA no Starship element calls for Coccidioides; >= 50% rule: NA no Starship element calls for Coccidioides.
| species | sm_type | n_clusters | n_with_captain_gene | pct_with_captain_gene |
|---|---|---|---|---|
| all | T1PKS | 1823 | 3 | 0.16 |
| all | terpene | 1287 | 9 | 0.70 |
| all | terpene-precursor | 1003 | 0 | 0.00 |
| all | NRPS | 671 | 0 | 0.00 |
| all | hybrid:NRP-metallophore+NRPS | 660 | 0 | 0.00 |
| all | NRPS-like | 400 | 0 | 0.00 |
| all | hybrid:NRPS+T1PKS | 354 | 0 | 0.00 |
| all | betalactone | 334 | 0 | 0.00 |
| all | T3PKS | 330 | 4 | 1.21 |
| all | fungal_CDPS | 328 | 0 | 0.00 |
| all | isocyanide | 318 | 0 | 0.00 |
| all | hybrid:NRPS+indole | 312 | 0 | 0.00 |
| all | hybrid:NRPS-like+T1PKS | 302 | 4 | 1.32 |
| all | hybrid:NRPS+T1PKS+terpene | 295 | 2 | 0.68 |
| all | isocyanide-nrp | 254 | 0 | 0.00 |
| all | hybrid:NRPS-like+T1PKS+terpene | 31 | 0 | 0.00 |
| all | RiPP-like | 3 | 0 | 0.00 |
| all | NI-siderophore | 3 | 0 | 0.00 |
| all | hybrid:NRPS+T3PKS | 2 | 0 | 0.00 |
| all | hybrid:T3PKS+isocyanide-nrp | 2 | 0 | 0.00 |
| all | hybrid:NRPS+T1PKS+fungal_CDPS | 2 | 0 | 0.00 |
| all | ranthipeptide | 2 | 0 | 0.00 |
| all | hybrid:NRPS+fungal_CDPS+indole | 1 | 0 | 0.00 |
| all | hybrid:T1PKS+T3PKS | 1 | 0 | 0.00 |
| all | hybrid:NRP-metallophore+NRPS+T1PKS | 1 | 0 | 0.00 |
| all | hybrid:isocyanide+terpene | 1 | 0 | 0.00 |
| all | hybrid:T1PKS+terpene | 1 | 0 | 0.00 |
| all | hybrid:T1PKS+fungal_CDPS | 1 | 0 | 0.00 |
| all | hybrid:T1PKS+isocyanide | 1 | 0 | 0.00 |
| all | hybrid:NRPS-like+T1PKS+fungal_CDPS | 1 | 0 | 0.00 |
| all | hybrid:NRP-metallophore+NRPS+isocyanide-nrp | 1 | 0 | 0.00 |
| all | hybrid:T1PKS+terpene-precursor | 1 | 0 | 0.00 |
| all | hybrid:NRPS-like+isocyanide | 1 | 0 | 0.00 |
| all | hybrid:NRPS-like+terpene-precursor | 1 | 0 | 0.00 |
| all | hybrid:NRP-metallophore+NRPS+betalactone | 1 | 0 | 0.00 |
| all | redox-cofactor | 1 | 0 | 0.00 |
| all | NAGGN | 1 | 0 | 0.00 |
| all | arylpolyene | 1 | 0 | 0.00 |
| all | phosphonate | 1 | 0 | 0.00 |
| all | hybrid:NRPS+NRPS-like | 1 | 0 | 0.00 |
| all | hybrid:azole-containing-RiPP+terpene | 1 | 0 | 0.00 |
| all | hybrid:NRPS+indole+terpene-precursor | 1 | 0 | 0.00 |
| all | fungal-RiPP | 1 | 0 | 0.00 |
| all | hybrid:NRPS+indole+isocyanide | 1 | 0 | 0.00 |
| all | hybrid:NRPS+T1PKS+terpene-precursor | 1 | 0 | 0.00 |
| Coccidioides immitis | T1PKS | 12 | 1 | 8.33 |
| Coccidioides immitis | terpene | 7 | 0 | 0.00 |
| Coccidioides immitis | terpene-precursor | 6 | 0 | 0.00 |
| Coccidioides immitis | NRPS | 4 | 0 | 0.00 |
| Coccidioides immitis | hybrid:NRP-metallophore+NRPS | 4 | 0 | 0.00 |
| Coccidioides immitis | NRPS-like | 3 | 0 | 0.00 |
| Coccidioides immitis | T3PKS | 2 | 0 | 0.00 |
| Coccidioides immitis | isocyanide | 2 | 0 | 0.00 |
| Coccidioides immitis | hybrid:NRPS+T1PKS+terpene | 2 | 0 | 0.00 |
| Coccidioides immitis | fungal_CDPS | 2 | 0 | 0.00 |
| Coccidioides immitis | hybrid:NRPS+indole | 2 | 0 | 0.00 |
| Coccidioides immitis | hybrid:NRPS-like+T1PKS | 2 | 0 | 0.00 |
| Coccidioides immitis | hybrid:NRPS+T1PKS | 2 | 0 | 0.00 |
| Coccidioides immitis | betalactone | 2 | 0 | 0.00 |
| Coccidioides immitis | isocyanide-nrp | 1 | 0 | 0.00 |
| Coccidioides posadasii | T1PKS | 1811 | 2 | 0.11 |
| Coccidioides posadasii | terpene | 1280 | 9 | 0.70 |
| Coccidioides posadasii | terpene-precursor | 997 | 0 | 0.00 |
| Coccidioides posadasii | NRPS | 667 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRP-metallophore+NRPS | 656 | 0 | 0.00 |
| Coccidioides posadasii | NRPS-like | 397 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+T1PKS | 352 | 0 | 0.00 |
| Coccidioides posadasii | betalactone | 332 | 0 | 0.00 |
| Coccidioides posadasii | T3PKS | 328 | 4 | 1.22 |
| Coccidioides posadasii | fungal_CDPS | 326 | 0 | 0.00 |
| Coccidioides posadasii | isocyanide | 316 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+indole | 310 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS-like+T1PKS | 300 | 4 | 1.33 |
| Coccidioides posadasii | hybrid:NRPS+T1PKS+terpene | 293 | 2 | 0.68 |
| Coccidioides posadasii | isocyanide-nrp | 253 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS-like+T1PKS+terpene | 31 | 0 | 0.00 |
| Coccidioides posadasii | RiPP-like | 3 | 0 | 0.00 |
| Coccidioides posadasii | NI-siderophore | 3 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+T3PKS | 2 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T3PKS+isocyanide-nrp | 2 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+T1PKS+fungal_CDPS | 2 | 0 | 0.00 |
| Coccidioides posadasii | ranthipeptide | 2 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+fungal_CDPS+indole | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T1PKS+T3PKS | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRP-metallophore+NRPS+T1PKS | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:isocyanide+terpene | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T1PKS+terpene | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T1PKS+fungal_CDPS | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T1PKS+isocyanide | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS-like+T1PKS+fungal_CDPS | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRP-metallophore+NRPS+isocyanide-nrp | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:T1PKS+terpene-precursor | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS-like+isocyanide | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS-like+terpene-precursor | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRP-metallophore+NRPS+betalactone | 1 | 0 | 0.00 |
| Coccidioides posadasii | redox-cofactor | 1 | 0 | 0.00 |
| Coccidioides posadasii | NAGGN | 1 | 0 | 0.00 |
| Coccidioides posadasii | arylpolyene | 1 | 0 | 0.00 |
| Coccidioides posadasii | phosphonate | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+NRPS-like | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:azole-containing-RiPP+terpene | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+indole+terpene-precursor | 1 | 0 | 0.00 |
| Coccidioides posadasii | fungal-RiPP | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+indole+isocyanide | 1 | 0 | 0.00 |
| Coccidioides posadasii | hybrid:NRPS+T1PKS+terpene-precursor | 1 | 0 | 0.00 |
SM summary metrics (sm_starship_overlap.tsv)
| metric | value | definition |
|---|---|---|
| strains_in_run | 362 | rows of the run samplesheet |
| strains_with_antismash | 335 | exact name match to an annotation dir with antiSMASH output |
| strains_without_antismash | Coahuila_2,UTAH_20380X1,UTAH_20380X2,UTAH_20380X5,UTAH_23742X12,UTAH_23742X144,UTAH_23742X160,UTAH_23742X163,UTAH_23742X165,UTAH_23742X168,UTAH_23742X18,UTAH_23742X189,UTAH_23742X19,UTAH_23742X195,UTAH_23742X199,UTAH_23742X208,UTAH_23742X209,UTAH_23742X246,UTAH_23742X253,UTAH_23742X38,UTAH_23742X40, | |
| sm_clusters | 8739 | antiSMASH 8.0.1 regions |
| sm_clusters_with_captain_gene | 22 | region CDS include a DUF3435 hit |
| sm_clusters_overlapping_starship_ge1gene | NA | no Starship element calls for Coccidioides |
| sm_clusters_overlapping_starship_ge50pct | NA | no Starship element calls for Coccidioides |
| genes_total | 2819145 | proteins in the included strains' annotations |
| captain_genes | 3674 | DUF3435 hits, E <= 1e-05 |
| genes_in_sm_clusters | 163152 | |
| captain_genes_in_sm_clusters | 26 | |
| expected_captain_genes_in_sm_clusters | 212.62 | K*n/N |
| p_hypergeom_greater | 1 | pooled over strains |
| p_hypergeom_less | 2.69e-61 | pooled over strains (depletion) |
Data and limits
- No genome of this run has Starship element coordinates. Captain-gene (DUF3435) families are a proxy: a captain gene marks a possible Starship, not its span.
- SM annotation: antiSMASH 8.0.1 regions.
- SM annotation source (PROVENANCE_sm.yaml):
/bigdata/stajichlab/shared/projects/Coccidioides/PopGenomics/2025_All_Cocci/Assembly/annotation/<strain>/{antismash_local,annotate_misc,annotate_results} (antiSMASH 8.0.1, funannotate 1.8.17; not the 20260112 freeze used by the pangenome runs). This page does not map SM cluster genes to the pangenome run's protein IDs or to islands. - Strains with SM annotation: 335 of 362.
- Provenance: PROVENANCE.yaml, PROVENANCE_sm.yaml, inputs_PROVENANCE.yaml.