MATPredict · mating-type report

PvariotiiCBS101075

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 01:48 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1medium confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-1 locus on RCNU01000001MAT1-1 locus: genes from left to right on RCNU01000001, 171,426 to 185,162: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).175 kb180 kb185 kb← 170.7 kb more to contig endcalled locusCOX13: conserved flank, 171,426–172,234 (-), identity 77.1%, search hit onlyCOX13APN2: conserved flank, 172,386–174,796 (+), identity 84.1%, search hit onlyAPN2MAT1-1-4: core MAT gene, 177,813–178,196 (-), identity 26.515%, search hit onlyMAT1-1-4MAT1-1-1: core MAT gene, 179,024–180,176 (+), identity 46.7%, search hit onlyMAT1-1-1SLA2: conserved flank, 181,217–185,162 (-), identity 90.8%, search hit onlySLA2
Gene order on RCNU01000001. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on RCNU01000001, 170,740 to 185,847C8Q69DRAFT_448989 171,032-172,343 (-): cytochrome c oxidase, subunit VIaC8Q69DRAFT_448989C8Q69DRAFT_489326 172,344-175,332 (+): XM_028632105.1C8Q69DRAFT_489326C8Q69DRAFT_449005 176,296-177,242 (-): XM_028629333.1C8Q69DRAFT_449005C8Q69DRAFT_511399 176,908-178,546 (-): XM_028633264.1C8Q69DRAFT_511399C8Q69DRAFT_439990 179,024-180,176 (+): MAT1-1-1C8Q69DRAFT_439990 MAT1-1-1C8Q69DRAFT_449012 180,765-185,366 (-): putative endocytosis protein end4C8Q69DRAFT_449012C8Q69DRAFT_449014 185,489-188,656 (-): PH domain-containing proteinC8Q69DRAFT_449014
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
RCNU01000001:171,426–185,162 · 13.7 kb
Own genes
RCNU01000001:171,426–185,162 · 13.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
171.4 kb
Region (samtools)
RCNU01000001:171426-185162
Idiomorph scores
  • MAT1-1 255.0

No other idiomorph scored.

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, proteome77.1cov 100.0%4.7e-72205 bits171,426–172,234 -–746128_af293_MAT_MAT1-2C8Q69DRAFT_448989
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%2.0e-276766 bits172,386–174,796 +–2903220_liq80xsp_MAT_combinedC8Q69DRAFT_489326
MAT1-1-4core MAThit onlytblastn26.5cov 47.0%4.4e-0750 bits177,813–178,196 -–199306_rmscc1040_MAT_MAT1-1C8Q69DRAFT_511399
MAT1-1-1core MAThit onlyDIAMOND, proteome46.7cov 30.4%5.2e-85255 bits179,024–180,176 +–1047171_ipo323_MAT_MAT1-1C8Q69DRAFT_439990 MAT1-1-1
SLA2conserved flankhit onlyDIAMOND, proteome90.8cov 100.0%< 1e-1801,575 bits181,217–185,162 -–107463_unknown-1_MAT_MAT1-2C8Q69DRAFT_449012

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
MATRCNU01000010:753,393–755,575MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
PvariotiiCBS101075.genome.fasta
Assembly
86 contigs · 30.1 Mb · N50 1.7 Mb
Genome SHA-256
1897897076bbbe8ba543b3143d5778f8c2a420594bdc890aa590f7a40fba9521
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': 1131624, '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 1131624', 'routed_by': 'family taxid 1131624 (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
2026-11-07T01:48:07Z
Run time
48 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