MATPredict · mating-type report

TmarneffeiATCC18224

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 01:55 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 DS995905MAT1-2 locus: genes from left to right on DS995905, 732,956 to 755,089: 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); MAT1-2-4 (core MAT gene, plus strand); CIMG_00407 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand); MAT1-2-10 (core MAT gene, plus strand).735 kb740 kb745 kb750 kb755 kb← 731.8 kb more to contig endcalled locusCOX13: conserved flank, 732,956–733,641 (-), identity 76.7%, search hit onlyCOX13APN2: conserved flank, 734,034–736,127 (+), identity 88.6%, search hit onlyAPN2MAT1-1-3: core MAT gene, 738,485–739,569 (-), identity 36.5%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 738,485–739,569 (-), identity 47.1%, search hit onlyMAT1-2-1MAT1-2-4: core MAT gene, 740,109–740,597 (+), identity 33.13%, gene modelMAT1-2-4CIMG_00407: core MAT gene, 740,505–740,597 (+), identity 32.258%, search hit onlyCIMG_00407SLA2: conserved flank, 744,745–748,639 (-), identity 88.8%, search hit onlySLA2MAT1-2-10: core MAT gene, 754,925–755,089 (+), identity 34.545%, search hit onlyMAT1-2-10
Gene order on DS995905. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on DS995905, 731,849 to 756,196PMAA_003170 731,458-732,587 (+): ThiJ/PfpI family proteinPMAA_003170PMAA_003180 732,723-733,696 (-): cytochrome c oxidase subunit VIa, putativePMAA_003180PMAA_003190 734,034-737,110 (+): DNA lyase Apn2PMAA_003190PMAA_003200 738,485-739,730 (-): mating type protein MAT1-2-1PMAA_003200PMAA_003210 740,109-740,842 (+): mating locus protein, putativePMAA_003210PMAA_003220 744,439-748,639 (-): cytoskeleton assembly control protein Sla2, putativePMAA_003220PMAA_003230 749,212-752,288 (-): conserved hypothetical proteinPMAA_003230PMAA_003240 752,893-754,268 (-): ankyrin repeat-containing protein, putativePMAA_003240PMAA_003250 754,801-758,136 (-): ubiquitin thiolesterase (OtuB1), putativePMAA_003250
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
  • gene model
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
DS995905:732,956–755,089 · 22.1 kb
Own genes
DS995905:732,956–755,089 · 22.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 8 gene hits
Nearest contig end
733.0 kb
Region (samtools)
DS995905:732956-755089
Idiomorph scores
  • MAT1-2 172.0

Margin over the set-aside MAT1-1-3 hit: 10.6 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
MAT1-2-147.1MAT1-1-336.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome76.7cov 85.1%1.5e-63184 bits732,956–733,641 -–162425_fgsc-a4_MAT_combinedPMAA_003180
APN2conserved flankhit onlyDIAMOND, proteome88.6cov 36.7%1.2e-265735 bits734,034–736,127 +–2903220_liq80xsp_MAT_combinedPMAA_003190
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome36.5cov 41.1%6.1e-1256 bits738,485–739,569 -–230073_uamh-1363_MAT_MAT1-1PMAA_003200
MAT1-2-1core MAThit onlyDIAMOND, proteome47.1cov 33.6%8.2e-54172 bits738,485–739,569 -–5518_3639_MAT_combinedPMAA_003200
MAT1-2-4core MATgene modelexonerate33.1cov 65.2%4.9e-2397 bits740,109–740,597 +1746128_af293_MAT_MAT1-2PMAA_003210
CIMG_00407core MAThit onlytblastn32.3cov 12.0%8.0e-0131 bits740,505–740,597 +–5501_rs_MAT_MAT1-2PMAA_003210
SLA2conserved flankhit onlyDIAMOND, proteome88.8cov 100.0%< 1e-1801,516 bits744,745–748,639 -–1301501_voucher-215_MAT_MAT1-1PMAA_003220
MAT1-2-10core MAThit onlytblastn34.5cov 13.0%2.4e+0030 bits754,925–755,089 +–28548_06cwm-g22_MAT_combinedPMAA_003250 (opposite strand)

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATDS995904:514,483–516,630MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
TmarneffeiATCC18224.genome.fasta
Assembly
453 contigs · 28.7 Mb · N50 3.3 Mb
Genome SHA-256
bb48e0aff46dad907fb5c7a89a50b8d9f0af1fbf1767cc0978c8dc557945f5b4
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': 28568, '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 28568', 'routed_by': 'family taxid 28568 (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
2026-11-07T01:55:01Z
Run time
52 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