MATPredict · mating-type report

TvirensGv29-8

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 02:37 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 ABDF02000006MAT1-2 locus: genes from left to right on ABDF02000006, 1,347,050 to 1,360,082: 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).1,350 kb1,355 kb1,360 kb← 1,346.4 kb more to contig endcalled locusSLA2: conserved flank, 1,347,050–1,350,478 (+), identity 81.6%, search hit onlySLA2COX13: conserved flank, 1,354,276–1,354,995 (-), identity 62.9%, search hit onlyCOX13APN2: conserved flank, 1,355,623–1,358,037 (+), identity 88.6%, search hit onlyAPN2MAT1-1-3: core MAT gene, 1,358,702–1,360,082 (-), identity 42.4%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,358,702–1,360,082 (-), identity 55.0%, search hit onlyMAT1-2-1
Gene order on ABDF02000006. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on ABDF02000006, 1,346,399 to 1,360,733TRIVIDRAFT_179842 1,346,877-1,350,671 (+): ANTH domain | I/LWEQ domain | domain-containing proteinTRIVIDRAFT_179842TRIVIDRAFT_54100 1,350,782-1,353,357 (-): Anaphase-promoting complex subunit 5 | domain-containing proteinTRIVIDRAFT_54100TRIVIDRAFT_110576 1,354,061-1,355,034 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinTRIVIDRAFT_110576TRIVIDRAFT_28020 1,355,623-1,358,037 (+): DNA lyaseTRIVIDRAFT_28020TRIVIDRAFT_60622 1,358,702-1,360,082 (-): MATa1 mating type proteinTRIVIDRAFT_60622
FungiDB release 71 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
ABDF02000006:1,347,050–1,360,082 · 13.0 kb
Own genes
ABDF02000006:1,347,050–1,360,082 · 13.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.3 Mb
Region (samtools)
ABDF02000006:1347050-1360082
Idiomorph scores
  • MAT1-2 139.0

Margin over the set-aside MAT1-1-3 hit: 12.6 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
MAT1-2-155.0MAT1-1-342.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,454 bits1,347,050–1,350,478 +–107463_unknown-1_MAT_MAT1-2TRIVIDRAFT_179842
COX13conserved flankhit onlyDIAMOND, proteome62.9cov 99.2%7.5e-60174 bits1,354,276–1,354,995 -–578113_sxlc146_MAT_MAT1-2TRIVIDRAFT_110576
APN2conserved flankhit onlyDIAMOND, proteome88.6cov 36.7%3.1e-217613 bits1,355,623–1,358,037 +–2903220_liq80xsp_MAT_combinedTRIVIDRAFT_28020
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome42.4cov 42.0%6.2e-1771 bits1,358,702–1,360,082 -–5518_3639_MAT_combinedTRIVIDRAFT_60622
MAT1-2-1core MAThit onlyDIAMOND, proteome55.0cov 76.2%1.1e-41139 bits1,358,702–1,360,082 -–61372_suf959_MAT_MAT1-2TRIVIDRAFT_60622

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
MATABDF02000004:952,963–953,190MAT1-2MAT1-2-11too few of the family's genes found
MATABDF02000071:94,386–94,611MAT1-2MAT1-2-11too few of the family's genes found
MATABDF02000090:45,309–45,602MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
TvirensGv29-8.genome.fasta
Assembly
93 contigs · 39.0 Mb · N50 1.8 Mb
Genome SHA-256
799c2ef58d01a5649e42eeb20c7f6670790e825be3227ad343cb58d47f82de53
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': 'genus', 'routing_taxid': 5129, '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 5129', 'routed_by': 'family taxid 5129 (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
2026-11-07T02:36:24Z
Run time
75 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