MATPredict · mating-type report

TmarneffeiTM4

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 02:56 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 CP015874MAT1-2 locus: genes from left to right on CP015874, 748,217 to 770,271: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-3 (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).750 kb755 kb760 kb765 kb770 kb← 747.1 kb more to contig endcalled locusCOX13: conserved flank, 748,217–748,878 (-), identity 75.0%, the two modelling tools disagreeCOX13APN2: conserved flank, 749,270–750,684 (+), identity 72.43%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 754,096–754,817 (-), identity 43.07%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 754,141–754,251 (-), identity 37.838%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-4: core MAT gene, 755,369–755,857 (+), identity 33.13%, gene modelMAT1-2-4CIMG_00407: core MAT gene, 755,765–755,857 (+), identity 32.258%, search hit onlyCIMG_00407SLA2: conserved flank, 759,909–763,748 (-), identity 86.91%, gene modelSLA2MAT1-2-10: core MAT gene, 770,107–770,271 (+), identity 34.545%, search hit onlyMAT1-2-10
Gene order on CP015874. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
Location
CP015874:748,217–770,271 · 22.1 kb
Own genes
CP015874:748,217–770,271 · 22.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 8 gene hits
Nearest contig end
748.2 kb
Region (samtools)
CP015874:748217-770271
Idiomorph scores
  • MAT1-2 97.4

Margin over the set-aside MAT1-1-3 hit: 17.7 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
MAT1-2-155.6MAT1-1-337.8100.0higher identity
MAT1-2-157.5MAT1-1-321.352.5higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankmodels differexonerateminiprot: 748,217–748,899, 73.2%75.0cov 96.3%7.6e-48164 bits748,217–748,878 -5746128_af293_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 749,270–751,371, 60.9%2 frameshiftsdefective gene model72.4cov 62.0%< 1e-180654 bits749,270–750,684 +5746128_a1163_MAT_MAT1-1
MAT1-2-1core MATmodels differexonerateminiprot: 753,997–754,817, 40.0%43.1cov 64.6%2.1e-3875 bits754,096–754,817 -3746128_af293_MAT_MAT1-2
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlytblastn37.8cov 21.0%1.3e-0640 bits754,141–754,251 -–230073_uamh-1363_MAT_MAT1-1
MAT1-2-4core MATgene modelexonerate33.1cov 65.2%4.8e-2397 bits755,369–755,857 +1746128_af293_MAT_MAT1-2
CIMG_00407core MAThit onlytblastn32.3cov 12.0%7.9e-0131 bits755,765–755,857 +–5501_rs_MAT_MAT1-2
SLA2conserved flankgene modelexonerate86.9cov 89.3%< 1e-180789 bits759,909–763,748 -11746128_a1163_MAT_MAT1-1
MAT1-2-10core MAThit onlytblastn34.5cov 13.0%2.4e+0030 bits770,107–770,271 +–28548_06cwm-g22_MAT_combined

Withheld candidate loci 17

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: fewer than 2 genes could be modelled (17).

Show the 17 withheld loci

Withheld loci (17)

familylocationidiomorph genesmodelledreason
MATCP015870:1,004,639–1,008,667MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATCP015870:1,081,359–1,093,153MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP015870:1,700,988–1,711,670MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATCP015870:1,952,740–1,964,581MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP015872:902,904–916,789MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATCP015872:2,798,455–2,811,598MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP015873:1,313,215–1,338,027MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATCP015873:1,672,472–1,699,690MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP015873:1,958,003–2,001,840MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP015875:1,255,143–1,257,831MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATCP015868:520,891–537,366MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATCP015868:954,893–981,074MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP015868:3,288,666–3,290,740MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP015869:3,808,553–3,824,881MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATCP015869:4,102,027–4,122,820MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP015871:415,300–424,199MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP015871:963,798–964,875MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled

Provenance

Genome file
TmarneffeiTM4.genome.fasta
Assembly
8 contigs · 28.3 Mb · N50 3.7 Mb
Genome SHA-256
1a6da0029a3a24ef6d6814085a26ded9974b3eabce1a340aae6b8c0294b55c26
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
2026-11-07T02:55:09Z
Run time
83 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