Result
Mating type
- alpha: MAT gene without flanking genes, medium confidence, 6.4 kb on KN905664. Gene order: STE3 · MFalpha · MFa.
Called loci 1
alpha MAT family · Basidiomycota
medium confidence- core MAT gene
- search hit only
- Location
- KN905664:
39,402–45,817 · 6.4 kb - Own genes
- KN905664:
39,402–45,817 · 6.4 kb - Locus
- A MAT gene with no flanking gene beside it; not a full locus.
- Genes modelled
- 2 of 3 gene hits
- Nearest contig end
- 165 bp
- Region (samtools)
KN905664:39402-45817
Idiomorph scores
- alpha 72.0
Margin over the set-aside MFa hit: 39.9 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.
| kept | identity % | set aside | identity % | overlap % | basis |
|---|---|---|---|---|---|
| MFalpha | 94.7 | MFa | 54.8 | 100.0 | higher identity |
Gene evidence
| Gene | Role | Model | Identity % | E-value | Position (strand) | Exons | Reference record | FungiDB gene |
|---|---|---|---|---|---|---|---|---|
| STE3 | core MAT | hit onlyDIAMOND, proteome | 90.5cov 100.0% | 5.0e-262703 bits | 39,402–40,720 + | – | 40410_ | I311_06454 |
| MFalpha | core MAT | hit onlyDIAMOND, proteome | 94.7cov 100.0% | 3.1e-2372 bits | 45,701–45,817 - | – | 40410_ | I311_06456 |
| MFa | core MATlost to MFalpha, not counted | hit onlytblastn | 54.8cov 100.0% | 2.2e-0640 bits | 45,704–45,817 - | – | 40410_ | I311_06456 |
| FAO1 | expected, not found | – | ||||||
| PAN6 | expected, not found | – | ||||||
| NOG2 | not searchable: no reference protein in the database | – | ||||||
| UAP1 | not searchable: no reference protein in the database | – | ||||||
What was searched
- Routing
- By taxonomy. The genome's taxonomy falls inside a curated family's scope; only those families were searched.
- Families searched
- Basidiomycota:MAT
- Genetic code
- 1
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
Withheld candidate loci 5
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 (5).
Show the 5 withheld loci
Withheld loci (5)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| MAT | KN905586: | undetermined | STE3 | 1 | too few of the family's genes found |
| MAT | KN905605: | undetermined | PAN6 | 1 | too few of the family's genes found |
| MAT | KN905629: | alpha | FAO1, SXI1, SXI2 | 3 | too few of the family's genes found |
| MAT | KN905702: | undetermined | RPL39 | 1 | too few of the family's genes found |
| MAT | KN905707: | alpha | MFalpha | 1 | too few of the family's genes found |
Provenance
- Genome file
- CgattiiNT10.genome.fasta
- Assembly
- 226 contigs · 18.0 Mb · N50 283.2 kb
- Genome SHA-256
- 9d3c969ffe8cb5e0fa636db5b9d63096fa69ac8e94f94ee75e484781049c6b9d
- MATPredict
- 0.8.1 (v0.8.1, 3a62e6302b)
- Database
- 86f18d232e4fe95d · 185 records
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
- Parameters
- phylum=Basidiomycota,
phylum_ guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'genus', 'routing_taxid': 1884633, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1884633', 'routed_by': 'family taxid 1884633 (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 supported_ min_ bitscore=33.0 - Run started
- 2026-11-07T02:19:15Z
- Run time
- 25 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
- MATPredict reads an assembly; it is not a mating assay. Two idiomorphs in one assembly can come from a homothallic species, a mixed culture or a merged diploid assembly.
- Fragmented assemblies can split a locus or lose its flanking genes; an uncalled genome is weak evidence of absence.
- Lineages with no curated record are searched with the whole phylum's references; family labels there are less reliable.