MATPredict · mating-type report

XarbusculaCBS124340

MAT locus above the FungiDB annotation (gene by gene)

organism not recorded

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 01:49 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on MU279353MAT1-2 locus: genes from left to right on MU279353, 474,768 to 488,011: SLA2 (conserved flank, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand).475 kb480 kb485 kb← 474.1 kb more to contig endcalled locusSLA2: conserved flank, 474,768–478,284 (+), identity 81.0%, search hit onlySLA2COX13: conserved flank, 479,050–479,866 (-), identity 65.0%, search hit onlyCOX13APN2: conserved flank, 480,431–482,586 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 486,590–488,011 (-), identity 31.5%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 486,590–488,011 (-), identity 48.9%, search hit onlyMAT1-2-1
Gene order on MU279353. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on MU279353, 474,106 to 488,672F4678DRAFT_430674 474,286-478,740 (+): ANTH domain-containing proteinF4678DRAFT_430674F4678DRAFT_430676 478,760-480,014 (-): cytochrome c oxidase, subunit VIaF4678DRAFT_430676F4678DRAFT_430678 480,141-482,759 (+): DNA lyaseF4678DRAFT_430678F4678DRAFT_478962 483,889-485,404 (-): unspecified productF4678DRAFT_478962F4678DRAFT_460793 486,590-488,011 (-): unspecified productF4678DRAFT_460793
FungiDB release 68 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • conserved flank
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
MU279353:474,768–488,011 · 13.2 kb
Own genes
MU279353:474,768–488,011 · 13.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
474.8 kb
Region (samtools)
MU279353:474768-488011
Idiomorph scores
  • MAT1-2 62.0

Margin over the set-aside MAT1-1-3 hit: 17.4 identity points (the narrowest overlap resolution below).

Score: bitscore of the best core-gene hit for each idiomorph.

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
MAT1-2-148.9MAT1-1-331.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome81.0cov 100.0%< 1e-1801,410 bits474,768–478,284 +–230073_uamh-1363_MAT_MAT1-1F4678DRAFT_430674
COX13conserved flankhit onlyDIAMOND, proteome65.0cov 99.2%2.5e-59172 bits479,050–479,866 -–578113_sxlc146_MAT_MAT1-2F4678DRAFT_430676
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%4.7e-233653 bits480,431–482,586 +–2903220_liq80xsp_MAT_combinedF4678DRAFT_430678
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome31.5cov 40.6%1.3e-0641 bits486,590–488,011 -–230073_uamh-1363_MAT_MAT1-1F4678DRAFT_460793
MAT1-2-1core MAThit onlyDIAMOND, proteome48.9cov 12.3%3.3e-1362 bits486,590–488,011 -–5141_unknown-1_MAT_MAT1-2F4678DRAFT_460793

Withheld candidate loci 3

Places with some MAT-gene evidence that did not pass a quality gate. Most genomes have several. They are listed so a known locus can be checked against them, not because they are likely calls.

Reasons: too few of the family's genes found (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATMU279357:828,760–829,176MAT1-2MAT1-2-11too few of the family's genes found
MATMU279357:929,639–932,426MAT1-2MAT1-2-11too few of the family's genes found
MATMU279360:280,571–282,699MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
XarbusculaCBS124340.genome.fasta
Assembly
89 contigs · 51.2 Mb · N50 1.1 Mb
Genome SHA-256
fa68da0676285d1ec9a3147d6bda035150dbbb2b8684012b14a20abe836e1c6f
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Ascomycota, phylum_guess={'requested': 'auto', 'status': 'low_confidence', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'family', 'routing_taxid': 37990, 'routing_taxid_rank': 'family', 'flags': [], 'gmg_version': 'gmg 0.3.2 (66055154a)', 'index': 'bfd-reps-2026.10.5-s20000.gmgi', 'index_sha256': '0f319567f1cab17643e1daf7ffdc0e3b312bd43913e351568108d67a4a19702c', 'index_spec': 'bfd-reps-2026.10.5-s20000.gmgi', 'note': 'GmG called phylum Ascomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 37990', 'routed_by': 'family taxid 37990 (lineage)'}, genetic_code=1, min_hits=2, require_core_role=True, max_polished_clusters_per_family=6, polish_strong_identity=50.0, polish_core_pair=True, partial_core_policy=off, homothallic_policy=off, confidence_cap_policy=off, cross_family_policy=off, fallback_after_withheld_policy=off, strong_single_gene_policy=off, scoped_roster_policy=off, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T01:47:57Z
Run time
66 s
Files
detection_report.yaml, detected_loci.gff3

Cite MATPredict as given in CITATION.cff at github.com/stajichlab/MATPredict. The reference records named in the gene tables are curated database entries; each record's metadata cites its source publication.

How to read this report

Idiomorph
The form of the mating-type locus a strain carries (for example MAT1-1 or MAT1-2, Plus or Minus). Basidiomycota HD and PR alleles are named after the reference they match.
High confidence
Every expected core MAT gene was found and modelled, with a conserved flanking gene where the family has one, on one contig.
Medium confidence
The core genes were found, but a gene could not be modelled, no conserved flank was found, or the locus is split (one step down).
Low confidence
A single isolated gene hit, or no core MAT gene.
Model status
Gene model: the reference protein was aligned to the genome to build the gene (exonerate, miniprot). Models differ: the two tools disagree on the structure; the alternate model is shown. Hit only: a search hit with no model, weaker evidence.
Identity
Percent amino-acid identity between the gene (or hit) and the closest reference protein.
Reference record
The curated database record whose protein matched best. Each record's metadata cites the publication or deposit it comes from.

Limits