MATPredict · mating-type report

CbeticolaCb09-40

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 02:37 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 NC_088936MAT1-1 locus: genes from left to right on NC_088936, 1,430,674 to 1,451,945: MAT1-1-1 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); COX13 (conserved flank, plus strand).1,430 kb1,435 kb1,440 kb1,445 kb1,450 kb← 1,429.6 kb more to contig endcalled locusMAT1-1-1: core MAT gene, 1,430,674–1,431,837 (+), identity 55.3%, search hit onlyMAT1-1-1MAT1-2-1: core MAT gene, 1,430,779–1,431,042 (+), identity 31.111%, search hit onlyMAT1-2-1 (lost to MAT1-1-1)COX13: conserved flank, 1,451,099–1,451,945 (+), identity 67.7%, search hit onlyCOX13
Gene order on NC_088936. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on NC_088936, 1,429,612 to 1,453,007RHO25_002568 1,430,674-1,431,837 (+): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinRHO25_002568RHO25_002569 1,432,219-1,432,920 (+): uncharacterized proteinRHO25_002569RHO25_002570 1,433,631-1,436,918 (+): uncharacterized proteinRHO25_002570RHO25_002571 1,437,053-1,438,694 (-): Alcohol dehydrogenase GroES-like domain | Zinc-binding dehydrogenase | domain-containing proteinRHO25_002571RHO25_002572 1,439,316-1,440,929 (+): Cytochrome P450 | domain-containing proteinRHO25_002572RHO25_002573 1,441,190-1,442,470 (-): Haloacid dehalogenase-like hydrolase | HAD-hyrolase-like | domain-containing proteinRHO25_002573RHO25_002574 1,442,778-1,445,846 (-): FACT complex subunit spt16RHO25_002574 SPT16RHO25_002575 1,446,372-1,447,650 (+): Mitochondrial carrier protein | domain-containing proteinRHO25_002575RHO25_002576 1,447,671-1,448,619 (-): uncharacterized proteinRHO25_002576RHO25_002577 1,449,344-1,450,696 (-): uncharacterized proteinRHO25_002577RHO25_002578 1,451,099-1,451,945 (+): Cytochrome c oxidase subunit VIa | domain-containing proteinRHO25_002578RHO25_002579 1,452,630-1,455,538 (-): MIR domain | Dolichyl-phosphate-mannose-protein mannosyltransferase | C-terminal four TMM region of protein-O-mannosyltransferase | domain-containing proteinRHO25_002579
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
NC_088936:1,430,674–1,451,945 · 21.3 kb
Own genes
NC_088936:1,430,674–1,451,945 · 21.3 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
2 of 3 gene hits
Nearest contig end
1.4 Mb
Region (samtools)
NC_088936:1430674-1451945
Idiomorph scores
  • MAT1-1 332.0

Margin over the set-aside MAT1-2-1 hit: 24.2 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
MAT1-1-155.3MAT1-2-131.1100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-1core MAThit onlyDIAMOND, proteome55.3cov 83.0%3.3e-115332 bits1,430,674–1,431,837 +–1873960_unknown-1_MAT_MAT1-1RHO25_002568
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-1, not countedhit onlytblastn31.1cov 25.0%6.5e-0132 bits1,430,779–1,431,042 +–13684_sn436ga98_MAT_MAT1-2RHO25_002568
COX13conserved flankhit onlyDIAMOND, proteome67.7cov 73.3%1.4e-50150 bits1,451,099–1,451,945 +–5501_rs_MAT_MAT1-2RHO25_002578
APN2expected, not found–
SLA2expected, not found–

Withheld candidate loci 6

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 (6).

Show the 6 withheld loci

Withheld loci (6)

familylocationidiomorph genesmodelledreason
MATNC_088935:252,823–255,078MAT1-2MAT1-2-11too few of the family's genes found
MATNC_088936:2,793,186–2,795,165undeterminedAPN21too few of the family's genes found
MATNC_088936:2,843,862–2,847,232undeterminedSLA21too few of the family's genes found
MATNC_088937:231,599–233,086MAT1-2MAT1-2-11too few of the family's genes found
MATNC_088939:188,599–191,909MAT1-1MAT1-1-1, MAT1-2-1, MAT1-1-32too few of the family's genes found
MATNC_088940:1,562,695–1,564,207MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CbeticolaCb09-40.genome.fasta
Assembly
10 contigs · 36.1 Mb · N50 4.2 Mb
Genome SHA-256
f2e40149e59101cc14e7d50ec4555d83a092c5f862c9c2b193b5231466ca745c
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': 93133, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 93133', 'routed_by': 'family taxid 93133 (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
2026-11-07T02:36:30Z
Run time
69 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