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Starships, islands and secondary-metabolite clusters

Source: bin/starship_island_overlap.py output for run immitis_in_posadasii_out_v5. 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.

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, 0 not mapped to a family of this run.

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	7078	70	4052	63	40.07	1.572	6.811	1.72e-09
captain	noncore	40324	354	9394	238	82.47	2.886	6.905	1.93e-69

Frequency bin and gain/loss direction (class_breakdown.tsv)

annotation	bin	direction	in_island	n_families
captain	cloud	ambiguous	yes	4
captain	cloud	gain	no	11
captain	cloud	gain	yes	54
captain	cloud	loss	yes	1
captain	core	conserved	no	3
captain	nonrep_only	gain	no	2
captain	nonrep_only	gain	yes	6
captain	outgroup_only	absent	no	85
captain	outgroup_only	absent	yes	109
captain	shell	ambiguous	yes	3
captain	shell	gain	no	2
captain	shell	gain	yes	25
captain	singleton	ambiguous	no	1
captain	singleton	ambiguous	yes	4
captain	singleton	gain	no	15
captain	singleton	gain	yes	32
captain	soft_core	gain	no	1

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.

SM summary metrics (sm_starship_overlap.tsv)

metric	value	definition
strains_in_run	529	rows of the run samplesheet
strains_with_antismash	479	exact name match to an annotation dir with antiSMASH output
strains_without_antismash	Coahuila_2,UTAH_20380X1,UTAH_20380X10,UTAH_20380X16,UTAH_20380X2,UTAH_20380X5,UTAH_23742X111,UTAH_23742X12,UTAH_23742X123,UTAH_23742X138,UTAH_23742X144,UTAH_23742X153,UTAH_23742X160,UTAH_23742X162,UTAH_23742X163,UTAH_23742X165,UTAH_23742X168,UTAH_23742X170,UTAH_23742X18,UTAH_23742X189,UTAH_23742X19,
sm_clusters	12528	antiSMASH 8.0.1 regions
sm_clusters_with_captain_gene	113	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	4047000	proteins in the included strains' annotations
captain_genes	5660	DUF3435 hits, E <= 1e-05
genes_in_sm_clusters	235390
captain_genes_in_sm_clusters	155
expected_captain_genes_in_sm_clusters	329.21	K*n/N
p_hypergeom_greater	1	pooled over strains
p_hypergeom_less	3.71e-28	pooled over strains (depletion)

Data and limits

Tables

• summary.tsv
• enrichment.tsv
• class_breakdown.tsv
• per_island.tsv.gz
• annotated_families.tsv.gz
• sm_by_type.tsv
• sm_starship_overlap.tsv
• sm_clusters.tsv.gz