MATPredict · mating-type report

NtetraspermaFGSC2508

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 02:09 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on GL891382MAT1-1 locus: genes from left to right on GL891382, 1,753,450 to 1,771,985: 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); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).1,755 kb1,760 kb1,765 kb1,770 kb← 1,752.5 kb more to contig endcalled locusCOX13: conserved flank, 1,753,450–1,754,381 (-), identity 72.6%, search hit onlyCOX13APN2: conserved flank, 1,755,302–1,757,394 (+), identity 81.8%, search hit onlyAPN2MAT1-1-3: core MAT gene, 1,759,015–1,760,151 (-), identity 97.2%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 1,759,324–1,759,626 (-), identity 25.743%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 1,760,900–1,762,246 (+), identity 94.6%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 1,762,645–1,763,640 (+), identity 98.0%, search hit onlyMAT1-1-1SLA2: conserved flank, 1,768,647–1,771,985 (-), identity 80.2%, search hit onlySLA2
Gene order on GL891382. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on GL891382, 1,752,524 to 1,772,912NEUTE1DRAFT_149499 1,750,301-1,752,961 (+): hypothetical proteinNEUTE1DRAFT_149499NEUTE1DRAFT_118541 1,753,181-1,754,530 (-): hypothetical proteinNEUTE1DRAFT_118541NEUTE1DRAFT_149501 1,755,302-1,757,684 (+): hypothetical proteinNEUTE1DRAFT_149501NEUTE1DRAFT_50737 1,759,015-1,760,151 (-): mating type proteinNEUTE1DRAFT_50737NEUTE1DRAFT_104830 1,760,900-1,762,246 (+): mating-type protein A-2 (Mt A-2)NEUTE1DRAFT_104830NEUTE1DRAFT_89543 1,762,645-1,763,863 (+): mating type proteinNEUTE1DRAFT_89543NEUTE1DRAFT_104832 1,768,139-1,768,339 (-): hypothetical proteinNEUTE1DRAFT_104832NEUTE1DRAFT_70857 1,768,397-1,771,986 (-): hypothetical proteinNEUTE1DRAFT_70857
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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
GL891382:1,753,450–1,771,985 · 18.5 kb
Own genes
GL891382:1,753,450–1,771,985 · 18.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
1.8 Mb
Region (samtools)
GL891382:1753450-1771985
Idiomorph scores
  • MAT1-1 713.0

Margin over the set-aside MAT1-2-1 hit: 71.5 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
MAT1-1-397.2MAT1-2-125.7100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome72.6cov 67.9%2.4e-51152 bits1,753,450–1,754,381 -–199306_rmscc1040_MAT_MAT1-1NEUTE1DRAFT_118541
APN2conserved flankhit onlyDIAMOND, proteome81.8cov 36.7%5.9e-221624 bits1,755,302–1,757,394 +–2903220_liq80xsp_MAT_combinedNEUTE1DRAFT_149501
MAT1-1-3core MAThit onlyDIAMOND, proteome97.2cov 99.7%4.8e-232625 bits1,759,015–1,760,151 -–5141_74-ors-a_MAT_MAT1-1NEUTE1DRAFT_50737
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn25.7cov 23.0%2.1e-0236 bits1,759,324–1,759,626 -–2903220_liq80xsp_MAT_combinedNEUTE1DRAFT_50737
MAT1-1-2core MAThit onlyDIAMOND, proteome94.6cov 100.0%2.7e-265713 bits1,760,900–1,762,246 +–5141_74-ors-a_MAT_MAT1-1NEUTE1DRAFT_104830
MAT1-1-1core MAThit onlyDIAMOND, proteome98.0cov 100.0%4.2e-219590 bits1,762,645–1,763,640 +–5141_74-ors-a_MAT_MAT1-1NEUTE1DRAFT_89543
SLA2conserved flankhit onlyDIAMOND, proteome80.2cov 100.0%< 1e-1801,325 bits1,768,647–1,771,985 -–230073_uamh-1363_MAT_MAT1-1NEUTE1DRAFT_70857

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
MATGL891305:3,708,555–3,746,822MAT1-2MAT1-2-1, MAT1-1-2, MAT1-2-41too few of the family's genes found
MATGL891306:2,655,774–2,658,019MAT1-2MAT1-2-1, MAT1-1-21too few of the family's genes found
MATGL891382:6,266,134–6,287,794MAT1-2MAT1-2-1, MAT1-1-21too few of the family's genes found

Provenance

Genome file
NtetraspermaFGSC2508.genome.fasta
Assembly
81 contigs · 39.1 Mb · N50 5.7 Mb
Genome SHA-256
f6fa2699a23ae2ac885c112833fb40c22d2cd1f7223fd82e3bebfd5707148a63
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': 'ok', 'usable': True, 'reason': None, 'phylum': 'Ascomycota', 'phylum_taxid': 4890, 'deepest_rank': 'species', 'routing_taxid': 5148, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 5148', 'routed_by': 'family taxid 5148 (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
2026-11-07T02:07:34Z
Run time
109 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