MATPredict · mating-type report

PrubensWisconsin54-1255

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 02:41 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 Pc00c20MAT1-1 locus: genes from left to right on Pc00c20, 1,753,589 to 1,771,151: MAT1-1-4 (core MAT gene, minus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).1,755 kb1,760 kb1,765 kb1,770 kb← 1,752.7 kb more to contig endcalled locusMAT1-1-4: core MAT gene, 1,753,589–1,753,711 (-), identity 39.024%, search hit onlyMAT1-1-4COX13: conserved flank, 1,760,299–1,761,100 (-), identity 78.9%, search hit onlyCOX13APN2: conserved flank, 1,761,420–1,763,660 (+), identity 84.1%, search hit onlyAPN2MAT1-1-1: core MAT gene, 1,765,021–1,766,097 (+), identity 41.0%, search hit onlyMAT1-1-1MAT1-2-1: core MAT gene, 1,765,306–1,765,638 (+), identity 24.786%, search hit onlyMAT1-2-1 (lost to MAT1-1-1)SLA2: conserved flank, 1,767,286–1,771,151 (-), identity 90.8%, search hit onlySLA2
Gene order on Pc00c20. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on Pc00c20, 1,752,712 to 1,772,028PCH_Pc20g07760 1,753,088-1,756,531 (-): Poly(ADP-ribose) polymerase catalytic domain | Ubiquitin-conjugating enzyme | domain-containing proteinPCH_Pc20g07760PCH_Pc20g07770 1,757,813-1,759,576 (+): unspecified productPCH_Pc20g07770PCH_Pc20g07780 1,760,299-1,761,100 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinPCH_Pc20g07780PCH_Pc20g07790 1,761,420-1,763,660 (+): DNA-(apurinic or apyrimidinic site) endonuclease 2PCH_Pc20g07790PCH_Pc20g07800 1,765,021-1,766,097 (+): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinPCH_Pc20g07800PCH_Pc20g07810 1,767,286-1,771,151 (-): ANTH domain | I/LWEQ domain | domain-containing proteinPCH_Pc20g07810PCH_Pc20g07820 1,771,847-1,774,700 (-): Maintenance of mitochondrial morphology protein 1 | Pleckstrin homology domain | domain-containing proteinPCH_Pc20g07820
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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
Pc00c20:1,753,589–1,771,151 · 17.6 kb
Own genes
Pc00c20:1,753,589–1,771,151 · 17.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
1.8 Mb
Region (samtools)
Pc00c20:1753589-1771151
Idiomorph scores
  • MAT1-1 101.0

Margin over the set-aside MAT1-2-1 hit: 16.2 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
MAT1-1-141.0MAT1-2-124.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-4core MAThit onlytblastn39.0cov 17.0%2.8e+0029 bits1,753,589–1,753,711 -–199306_rmscc1040_MAT_MAT1-1PCH_Pc20g07760
COX13conserved flankhit onlyDIAMOND, proteome78.9cov 87.3%2.9e-73208 bits1,760,299–1,761,100 -–162425_fgsc-a4_MAT_combinedPCH_Pc20g07780
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%4.9e-280774 bits1,761,420–1,763,660 +–2903220_liq80xsp_MAT_combinedPCH_Pc20g07790
MAT1-1-1core MAThit onlyDIAMOND, proteome41.0cov 35.5%9.7e-27101 bits1,765,021–1,766,097 +–199306_rmscc1040_MAT_MAT1-1PCH_Pc20g07800
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn24.8cov 35.0%1.8e-0134 bits1,765,306–1,765,638 +–578113_sxlc146_MAT_MAT1-2PCH_Pc20g07800
SLA2conserved flankhit onlyDIAMOND, proteome90.8cov 100.0%< 1e-1801,627 bits1,767,286–1,771,151 -–746128_af293_MAT_MAT1-2PCH_Pc20g07810

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
MATPc00c18:1,574,676–1,575,455MAT1-1MAT1-1-31too few of the family's genes found
MATPc00c22:1,301,320–1,302,967MAT1-2MAT1-2-11too few of the family's genes found
MATPc00c22:1,656,687–1,675,194MAT1-2MAT1-2-1, MAT1-1-21too few of the family's genes found

Provenance

Genome file
PrubensWisconsin54-1255.genome.fasta
Assembly
49 contigs · 32.2 Mb · N50 3.9 Mb
Genome SHA-256
b9fc5429dbd547063f7d05d031a40c5fc0d257181dc86edfc87dbe6a0df8155c
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': 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
2026-11-07T02:40:15Z
Run time
72 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