MATPredict · mating-type report

AfischeriNRRL181

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 02:03 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-1high confidenceMAT1-2medium confidence

Called loci 2

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on DS027690MAT1-1 locus: genes from left to right on DS027690, 2,661,927 to 2,675,129: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).2,665 kb2,670 kb2,675 kb253.4 kb more to contig end →called locusCOX13: conserved flank, 2,661,927–2,662,667 (-), identity 94.9%, search hit onlyCOX13APN2: conserved flank, 2,663,048–2,665,215 (+), identity 93.2%, search hit onlyAPN2MAT1-2-1: core MAT gene, 2,666,132–2,667,149 (-), identity 84.9%, search hit onlyMAT1-2-1MAT1-1-1: core MAT gene, 2,667,284–2,668,441 (+), identity 95.9%, search hit onlyMAT1-1-1SLA2: conserved flank, 2,670,931–2,675,129 (-), identity 95.1%, search hit onlySLA2
Gene order on DS027690. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on DS027690, 2,661,267 to 2,675,789NFIA_071060 2,659,009-2,661,524 (+): anaphase-promoting complex proteinNFIA_071060NFIA_071070 2,661,927-2,662,667 (-): cytochrome c oxidase subunit VIa, putativeNFIA_071070NFIA_071080 2,663,048-2,665,215 (+): DNA lyase, putativeNFIA_071080NFIA_071090 2,666,132-2,667,149 (-): mating-type protein, putativeNFIA_071090NFIA_071100 2,667,284-2,668,441 (+): mating-type protein MAT alpha 1NFIA_071100NFIA_071110 2,670,931-2,675,129 (-): cytoskeleton assembly control protein Sla2, putativeNFIA_071110NFIA_071120 2,675,576-2,678,402 (-): conserved hypothetical proteinNFIA_071120
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
Location
DS027690:2,661,927–2,675,129 · 13.2 kb
Own genes
DS027690:2,661,927–2,675,129 · 13.2 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 5 gene hits
Nearest contig end
254.1 kb
Region (samtools)
DS027690:2661927-2675129
Idiomorph scores
  • MAT1-1 706.0
  • MAT1-2 133.0

Margin over the next idiomorph: 573.0

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome94.9cov 100.0%5.0e-91253 bits2,661,927–2,662,667 -–746128_af293_MAT_MAT1-2NFIA_071070
APN2conserved flankhit onlyDIAMOND, proteome93.2cov 36.7%< 1e-1801,149 bits2,663,048–2,665,215 +–2903220_liq80xsp_MAT_combinedNFIA_071080
MAT1-2-1core MAThit onlyDIAMOND, proteome84.9cov 22.7%5.6e-40133 bits2,666,132–2,667,149 -–746128_af293_MAT_MAT1-2NFIA_071090
MAT1-1-1core MAThit onlyDIAMOND, proteome95.9cov 100.0%2.0e-262706 bits2,667,284–2,668,441 +–746128_a1163_MAT_MAT1-1NFIA_071100
SLA2conserved flankhit onlyDIAMOND, proteome95.1cov 100.0%< 1e-1801,801 bits2,670,931–2,675,129 -–746128_af293_MAT_MAT1-2NFIA_071110

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on DS027689MAT1-2 locus: genes from left to right on DS027689, 394,534 to 398,923: 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).395 kb396 kb397 kb398 kb399 kbcontig endcalled locusAPN2: conserved flank, 394,534–395,277 (+), identity 74.5%, search hit onlyAPN2MAT1-1-3: core MAT gene, 396,204–397,280 (-), identity 37.8%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 396,204–397,280 (-), identity 79.2%, search hit onlyMAT1-2-1MAT1-2-4: core MAT gene, 397,799–398,923 (+), identity 86.3%, search hit onlyMAT1-2-4CIMG_00407: core MAT gene, 398,392–398,616 (+), identity 28.0%, search hit onlyCIMG_00407
Gene order on DS027689. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on DS027689, 394,234 to 399,447NFIA_024380 394,534-395,277 (+): DNA lyase-like protein, putativeNFIA_024380NFIA_024390 396,204-397,280 (-): mating-type protein MAT1-2NFIA_024390NFIA_024400 397,799-398,923 (+): mating locus protein, putativeNFIA_024400
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
DS027689:394,534–398,923 · 4.4 kb
Own genes
DS027689:394,534–398,923 · 4.4 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
3 of 5 gene hits
Nearest contig end
524 bp
Region (samtools)
DS027689:394534-398923
Idiomorph scores
  • MAT1-2 513.0

Margin over the set-aside MAT1-1-3 hit: 41.4 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
MAT1-2-179.2MAT1-1-337.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
APN2conserved flankhit onlyDIAMOND, proteome74.5cov 90.4%1.1e-102305 bits394,534–395,277 +–27339_unknown-1_MAT_MAT1-2NFIA_024380
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome37.8cov 41.1%5.9e-1256 bits396,204–397,280 -–230073_uamh-1363_MAT_MAT1-1NFIA_024390
MAT1-2-1core MAThit onlyDIAMOND, proteome79.2cov 100.0%1.3e-187513 bits396,204–397,280 -–746128_af293_MAT_MAT1-2NFIA_024390
MAT1-2-4core MAThit onlyDIAMOND, proteome86.3cov 99.2%6.9e-160437 bits397,799–398,923 +–746128_af293_MAT_MAT1-2NFIA_024400
CIMG_00407core MAThit onlytblastn28.0cov 22.0%2.6e-0840 bits398,392–398,616 +–5501_rs_MAT_MAT1-2NFIA_024400
SLA2expected, not found–
COX13expected, not found–

Withheld candidate loci 2

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 (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATDS027685:1,133,463–1,136,439MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATDS027693:816,644–816,916MAT1-1MAT1-1-1, MAT1-1-31too few of the family's genes found

Provenance

Genome file
AfischeriNRRL181.genome.fasta
Assembly
163 contigs · 31.4 Mb · N50 2.9 Mb
Genome SHA-256
72d25e73b0baeadceb4388e47b1b29acd9935eff95724b19a8c83f1ad18deccd
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': 1131492, '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 1131492', 'routed_by': 'family taxid 1131492 (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
2026-11-07T02:02:06Z
Run time
70 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