Starships, islands and secondary-metabolite clusters
Source: bin/starship_island_overlap.py output for run full_v072. 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 |
|---|---|---|---|---|
| 47954 | 11676 | 4709 | 11683 | 5844 |
Starship families in islands
Starship family: a family with >= 1 gene of Asfu_Af293 whose midpoint lies inside one of 8 element(s) (7 high confidence).
| 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) |
|---|---|---|---|---|---|---|---|---|
| Starship families, all elements | 167 | 163 | 56 | 984 of 11676 | 163 of 163 (1.0) | 11683 of 40122 (0.2912) | 3.434 | 2.04e-88 |
| Starship families, high-confidence elements | 161 | 157 | 54 | 898 of 11676 | 157 of 157 (1.0) | 11683 of 40122 (0.2912) | 3.434 | 3.55e-85 |
All universes (enrichment.tsv)
| annotation | universe | N_universe | K_annotated | n_island | k_both | expected_k | fold | odds_ratio | p_hypergeom_greater |
|---|---|---|---|---|---|---|---|---|---|
| starship_all | cooc_eligible | 8452 | 91 | 5681 | 91 | 61.17 | 1.488 | inf | 1.57e-16 |
| starship_all | cooc_eligible_in_annotated_strain | 1945 | 91 | 1407 | 91 | 65.83 | 1.382 | inf | 6.92e-14 |
| starship_all | noncore | 40122 | 163 | 11683 | 163 | 47.46 | 3.434 | inf | 2.04e-88 |
| starship_all | noncore_in_annotated_strain | 3017 | 163 | 1707 | 163 | 92.22 | 1.767 | inf | 1.41e-42 |
| starship_high | cooc_eligible | 8452 | 87 | 5681 | 87 | 58.48 | 1.488 | inf | 7.85e-16 |
| starship_high | cooc_eligible_in_annotated_strain | 1945 | 87 | 1407 | 87 | 62.94 | 1.382 | inf | 2.72e-13 |
| starship_high | noncore | 40122 | 157 | 11683 | 157 | 45.72 | 3.434 | inf | 3.55e-85 |
| starship_high | noncore_in_annotated_strain | 3017 | 157 | 1707 | 157 | 88.83 | 1.767 | inf | 5.57e-41 |
Coordinate checks in the annotated strain
| metric | value | definition |
|---|---|---|
| n_island_instances_in_annotated_strains | 364 | non-core runs in annotated strains equal to an island member set |
| n_islands_overlapping_element_in_annotated_strain | 9 | islands with an instance in an annotated strain overlapping an element by >= 1 bp |
| n_high_elements_hit_family_level | 7 | |
| n_high_elements_overlapped_by_instance | 7 | |
| island_gene_frac_in_starship_sweep_metric | 0.2135 | sum over islands of annotated-strain genes of member families inside elements / all such genes (3587/16803) |
| noncore_gene_frac_in_starship_sweep_metric | 0.0581 | annotated-strain genes of non-core families inside elements (168/2893) |
Coordinate permutation
| statistic | observed | observed_noncore_genes_inside | n_perm | seed | null_mean | null_q95 | null_max | p_perm_greater |
|---|---|---|---|---|---|---|---|---|
| annotated-strain genes in island families inside elements | 168 | 168 | 1000 | 20261017 | 48.11 | 82 | 112 | 0.001 |
Per element
| element_id | label | confidence | contig | start | end | length_bp | n_genes | n_families | n_noncore_families | n_families_in_island | frac_families_in_island | n_islands_hit_family_level | n_island_instances_overlapping | frac_genes_inside_island_instances | bins |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AF293_e00029 | Lamia h4 | high | CM000169.1 | 6458 | 394211 | 387754 | 68 | 68 | 64 | 64 | 0.9412 | 306 | 2 | 0.9412 | cloud:37;core:3;shell:11;singleton:16;soft_core:1 |
| AF293_e00039 | Gnosis h1 | high | CM000174.1 | 2214324 | 2290180 | 75857 | 21 | 21 | 21 | 21 | 1.0 | 219 | 1 | 1.0 | cloud:12;shell:9 |
| AF293_e00041 | Janus (likely) h2 (likely) | unknown | CM000175.1 | 1807654 | 1860556 | 52903 | 6 | 6 | 6 | 6 | 1.0 | 93 | 1 | 1.0 | cloud:4;shell:1;singleton:1 |
| AF293_s00031 | Nebuchadnezzar h2 | high | CM000169.1 | 4343057 | 4400402 | 57346 | 20 | 20 | 20 | 20 | 1.0 | 24 | 1 | 1.0 | cloud:16;singleton:4 |
| AF293_s00032 | Osiris h4 | high | CM000171.1 | 639099 | 688497 | 49399 | 12 | 12 | 12 | 12 | 1.0 | 118 | 1 | 1.0 | cloud:1;shell:10;singleton:1 |
| AF293_s00035 | Osiris h3 | high | CM000171.1 | 1012445 | 1089733 | 77289 | 3 | 3 | 3 | 3 | 1.0 | 21 | 1 | 1.0 | cloud:1;singleton:2 |
| AF293_s00037 | Nebuchadnezzar h1 | high | CM000173.1 | 3842374 | 3895486 | 53113 | 17 | 17 | 17 | 17 | 1.0 | 48 | 1 | 1.0 | cloud:17 |
| AF293_s00042 | Tardis h1 | high | CM000176.1 | 1455665 | 1544699 | 89035 | 25 | 25 | 25 | 25 | 1.0 | 196 | 1 | 1.0 | cloud:14;shell:9;singleton:2 |
Captain-gene families (non-core) in islands
Captain gene: tblout targets with full-sequence E <= 1e-05; 2233 hits, 0 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 | 218 | 122 | 46 | 906 of 11676 | 122 of 217 (0.5622) | 11683 of 40122 (0.2912) | 1.931 | 6.78e-17 |
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 | 8452 | 45 | 5681 | 45 | 30.25 | 1.488 | inf | 1.63e-08 |
| captain | noncore | 40122 | 217 | 11683 | 122 | 63.19 | 1.931 | 3.148 | 6.78e-17 |
Frequency bin and gain/loss direction (class_breakdown.tsv)
| annotation | bin | direction | in_island | n_families |
|---|---|---|---|---|
| starship_all | cloud | ambiguous | yes | 4 |
| starship_all | cloud | gain | yes | 93 |
| starship_all | core | conserved | no | 3 |
| starship_all | shell | ambiguous | yes | 1 |
| starship_all | shell | gain | yes | 38 |
| starship_all | shell | loss | yes | 1 |
| starship_all | singleton | gain | yes | 26 |
| starship_all | soft_core | loss | no | 1 |
| starship_high | cloud | ambiguous | yes | 4 |
| starship_high | cloud | gain | yes | 89 |
| starship_high | core | conserved | no | 3 |
| starship_high | shell | ambiguous | yes | 1 |
| starship_high | shell | gain | yes | 37 |
| starship_high | shell | loss | yes | 1 |
| starship_high | singleton | gain | yes | 25 |
| starship_high | soft_core | loss | no | 1 |
| captain | cloud | ambiguous | yes | 4 |
| captain | cloud | gain | no | 15 |
| captain | cloud | gain | yes | 64 |
| captain | core | conserved | no | 1 |
| captain | nonrep_only | gain | no | 21 |
| captain | nonrep_only | gain | yes | 8 |
| captain | outgroup_only | absent | no | 3 |
| captain | outgroup_only | absent | yes | 2 |
| captain | shell | gain | yes | 20 |
| captain | singleton | ambiguous | no | 1 |
| captain | singleton | gain | no | 55 |
| captain | singleton | gain | yes | 24 |
Families in islands by annotation set (per element when element coordinates exist).
Secondary-metabolite (SM) clusters
Source: antiSMASH 8.0.4 regions.
SM key metrics
| metric | value | definition / source |
|---|---|---|
| antismash_version | 8.0.4 | Af293.json.gz |
| sm_clusters | 44 | antiSMASH regions (sm_clusters.tsv.gz) |
| sm_clusters_overlap_ge1gene | 3 | rule A (sm_clusters.tsv.gz) |
| sm_clusters_overlap_ge50pct | 1 | rule B (sm_clusters.tsv.gz) |
| sm_clusters_with_captain | 3 | DUF3435 hit E<=1e-5 in a cluster gene |
| sm_cluster_genes | 873 | CDS inside regions |
| sm_core_genes | 66 | CDS with a rule definition domain |
| elements_with_sm_cluster_ge1gene | 3 | sm_starship_overlap.tsv |
| elements_with_sm_cluster_ge50pct | 1 | sm_starship_overlap.tsv |
| hypergeom_sm_cluster_genes_in_starships_k | 28 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_expected | 16.05 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_p_greater | 0.00247 | universe: all Af293 CDS |
| sm_core_families | 65 | families of core genes (sm_core_families.tsv.gz) |
| sm_core_families_noncore | 15 | |
| sm_core_families_noncore_in_island | 10 | |
| hypergeom_core_families_in_islands_noncore_expected | 4.37 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_p_greater | 0.00286 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_k | 212 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_K | 310 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_expected | 90.27 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_p_greater | 1.39e-46 | universe: non-core families; K = SM families (Af293 genes); n = island families |
SM clusters by type
| type | n_clusters | n_overlap_ge1gene | n_overlap_ge50pct | n_with_captain |
|---|---|---|---|---|
| terpene | 12 | 1 | 0 | 1 |
| T1PKS | 8 | 1 | 1 | 1 |
| NRPS | 6 | 0 | 0 | 0 |
| NRPS-like | 4 | 0 | 0 | 0 |
| T1PKS+terpene | 2 | 0 | 0 | 0 |
| isocyanide | 2 | 0 | 0 | 0 |
| terpene-precursor | 2 | 0 | 0 | 0 |
| NRPS+indole | 1 | 0 | 0 | 0 |
| NRPS+indole+T1PKS+terpene | 1 | 0 | 0 | 0 |
| NRPS+terpene | 1 | 0 | 0 | 0 |
| T1PKS+NRPS-like | 1 | 1 | 0 | 1 |
| T1PKS+indole+terpene | 1 | 0 | 0 | 0 |
| betalactone | 1 | 0 | 0 | 0 |
| indole | 1 | 0 | 0 | 0 |
| isocyanide-nrp+NRPS | 1 | 0 | 0 | 0 |
| ALL | 44 | 3 | 1 | 3 |
Table S7 elements and SM clusters
| element_id | label | confidence | contig | start | end | n_genes_in_element | n_sm_clusters_ge1gene | n_sm_clusters_ge50pct | sm_clusters | n_sm_cluster_genes_in_element | captain_genes_in_element |
|---|---|---|---|---|---|---|---|---|---|---|---|
| AF293_e00029 | Lamia h4 | high | CM000169.1 | 6458 | 394211 | 71 | 1 | 1 | CM000169.1.region001(T1PKS;13/13 genes) | 13 | AFUA_1G00890 |
| AF293_e00039 | Gnosis h1 | high | CM000174.1 | 2214324 | 2290180 | 21 | 0 | 0 | 0 | AFUA_6G09300 | |
| AF293_e00041 | Janus (likely) h2 (likely) | unknown | CM000175.1 | 1807654 | 1860556 | 6 | 0 | 0 | 0 | ||
| AF293_s00031 | Nebuchadnezzar h2 | high | CM000169.1 | 4343057 | 4400402 | 20 | 0 | 0 | 0 | AFUA_1G16170 | |
| AF293_s00032 | Osiris h4 | high | CM000171.1 | 639099 | 688497 | 12 | 1 | 0 | CM000171.1.region002(T1PKS+NRPS-like;12/30 genes) | 12 | AFUA_3G02550 |
| AF293_s00035 | Osiris h3 | high | CM000171.1 | 1012445 | 1089733 | 3 | 0 | 0 | 0 | ||
| AF293_s00037 | Nebuchadnezzar h1 | high | CM000173.1 | 3842374 | 3895486 | 19 | 1 | 0 | CM000173.1.region009(terpene;3/7 genes) | 3 | AFUA_5G15040 |
| AF293_s00042 | Tardis h1 | high | CM000176.1 | 1455665 | 1544699 | 25 | 0 | 0 | 0 | AFUA_8G06132 |
SM cluster position permutation
| statistic | observed | n_perm | seed | null_mean | null_q95 | null_max | p_perm_greater | p_perm_less |
|---|---|---|---|---|---|---|---|---|
| clusters_overlap_ge1gene | 3 | 1000 | 20261017 | 1.884 | 4 | 6 | 0.28272 | 0.8951 |
| clusters_overlap_ge50pct | 1 | 1000 | 20261017 | 1.206 | 3 | 5 | 0.71528 | 0.64036 |
| sm_cluster_genes_in_elements | 28 | 1000 | 20261017 | 24.019 | 62 | 93 | 0.38262 | 0.63636 |
SM core-gene families by class, direction and island (sm_family_class_direction.tsv)
| gene_set | bin | direction | in_island | n_families |
|---|---|---|---|---|
| core_gene_families | cloud | gain | no | 3 |
| core_gene_families | cloud | gain | yes | 3 |
| core_gene_families | core | conserved | no | 44 |
| core_gene_families | shell | ambiguous | yes | 1 |
| core_gene_families | shell | gain | no | 1 |
| core_gene_families | shell | gain | yes | 3 |
| core_gene_families | shell | loss | yes | 2 |
| core_gene_families | singleton | gain | no | 1 |
| core_gene_families | singleton | gain | yes | 1 |
| core_gene_families | soft_core | ambiguous | no | 1 |
| core_gene_families | soft_core | gain | no | 3 |
| core_gene_families | soft_core | loss | no | 2 |
| all_cluster_gene_families | cloud | ambiguous | no | 4 |
| all_cluster_gene_families | cloud | ambiguous | yes | 9 |
| all_cluster_gene_families | cloud | gain | no | 56 |
| all_cluster_gene_families | cloud | gain | yes | 71 |
| all_cluster_gene_families | cloud | loss | no | 3 |
| all_cluster_gene_families | cloud | loss | yes | 2 |
| all_cluster_gene_families | core | conserved | no | 519 |
| all_cluster_gene_families | shell | ambiguous | no | 5 |
| all_cluster_gene_families | shell | ambiguous | yes | 20 |
| all_cluster_gene_families | shell | gain | no | 17 |
| all_cluster_gene_families | shell | gain | yes | 80 |
| all_cluster_gene_families | shell | loss | no | 4 |
| all_cluster_gene_families | shell | loss | yes | 23 |
| all_cluster_gene_families | singleton | gain | no | 9 |
| all_cluster_gene_families | singleton | gain | yes | 7 |
| all_cluster_gene_families | soft_core | ambiguous | no | 6 |
| all_cluster_gene_families | soft_core | gain | no | 17 |
| all_cluster_gene_families | soft_core | loss | no | 18 |
All SM summary metrics
| metric | value | definition / source |
|---|---|---|
| antismash_version | 8.0.4 | Af293.json.gz |
| af293_cds_in_antismash | 9630 | CDS features in antiSMASH JSON (from GFF3) |
| af293_cds_mapped_to_member | 9627 | coord:9623; fasta_GN:4; none:3 |
| af293_cds_with_family | 9627 | member in tier1_cluster.tsv |
| sm_clusters | 44 | antiSMASH regions (sm_clusters.tsv.gz) |
| sm_cluster_genes | 873 | CDS inside regions |
| sm_core_genes | 66 | CDS with a rule definition domain |
| sm_clusters_contig_edge | 3 | region qualifier contig_edge |
| starship_elements | 8 | Table S7 (inputs/af293_starships_table_s7.elements.tsv) |
| af293_cds_in_starships | 177 | CDS midpoint inside an element |
| sm_clusters_overlap_ge1gene | 3 | rule A (sm_clusters.tsv.gz) |
| sm_clusters_overlap_ge50pct | 1 | rule B (sm_clusters.tsv.gz) |
| sm_clusters_with_captain | 3 | DUF3435 hit E<=1e-5 in a cluster gene |
| af293_captain_cds | 7 | Af293 CDS whose member has a DUF3435 hit |
| elements_with_sm_cluster_ge1gene | 3 | sm_starship_overlap.tsv |
| elements_with_sm_cluster_ge50pct | 1 | sm_starship_overlap.tsv |
| perm_clusters_overlap_ge1gene_observed | 3 | sm_permutation.tsv |
| perm_clusters_overlap_ge1gene_null_mean | 1.884 | sm_permutation.tsv |
| perm_clusters_overlap_ge1gene_p_greater | 0.28272 | sm_permutation.tsv |
| perm_clusters_overlap_ge1gene_p_less | 0.8951 | sm_permutation.tsv |
| perm_clusters_overlap_ge50pct_observed | 1 | sm_permutation.tsv |
| perm_clusters_overlap_ge50pct_null_mean | 1.206 | sm_permutation.tsv |
| perm_clusters_overlap_ge50pct_p_greater | 0.71528 | sm_permutation.tsv |
| perm_clusters_overlap_ge50pct_p_less | 0.64036 | sm_permutation.tsv |
| perm_sm_cluster_genes_in_elements_observed | 28 | sm_permutation.tsv |
| perm_sm_cluster_genes_in_elements_null_mean | 24.019 | sm_permutation.tsv |
| perm_sm_cluster_genes_in_elements_p_greater | 0.38262 | sm_permutation.tsv |
| perm_sm_cluster_genes_in_elements_p_less | 0.63636 | sm_permutation.tsv |
| hypergeom_sm_cluster_genes_in_starships_N | 9630 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_K | 177 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_n | 873 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_k | 28 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_expected | 16.05 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_fold | 1.75 | universe: all Af293 CDS |
| hypergeom_sm_cluster_genes_in_starships_p_greater | 0.00247 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_N | 9630 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_K | 177 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_n | 66 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_k | 2 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_expected | 1.21 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_fold | 1.65 | universe: all Af293 CDS |
| hypergeom_sm_core_genes_in_starships_p_greater | 0.343 | universe: all Af293 CDS |
| hypergeom_core_families_in_islands_noncore_N | 40122 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_K | 15 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_n | 11683 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_k | 10 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_expected | 4.37 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_fold | 2.29 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_core_families_in_islands_noncore_p_greater | 0.00286 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_N | 40122 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_K | 310 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_n | 11683 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_k | 212 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_expected | 90.27 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_fold | 2.35 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| hypergeom_cluster_gene_families_in_islands_noncore_p_greater | 1.39e-46 | universe: non-core families; K = SM families (Af293 genes); n = island families |
| sm_core_families | 65 | families of core genes (sm_core_families.tsv.gz) |
| sm_core_families_noncore | 15 | |
| sm_core_families_noncore_in_island | 10 | |
| proxy_backbone_genes | 32 | full_v072/with_unplaced_af293_coords/sm_backbone_af293_genes.tsv.gz |
| proxy_backbone_genes_in_antismash_region | 28 | proxy gene member -> locus tag in a region |
| proxy_backbone_genes_antismash_core | 27 | proxy gene is an antiSMASH core gene |
| proxy_backbone_genes_in_starships | 2 | proxy result |
Data and limits
- Starship element coordinates exist only for Asfu_Af293 (8 elements). Family-level results transfer these calls to all strains through family membership; coordinate-level results apply to that strain only.
- SM annotation: antiSMASH 8.0.4 regions.
- SM cluster genes are mapped to pangenome families of this run (af293_cds_mapped_to_member: 9627 of 9630 CDS); see sm_family_class_direction.tsv.
- Provenance: PROVENANCE.yaml, PROVENANCE_sm.yaml, PROVENANCE_sm_analysis.yaml, inputs_PROVENANCE.yaml.