Result
Mating type
- undetermined: complete locus, high confidence, 13.5 kb on PchrRP-78_
SC013 . Gene order: beta_fg · HD1 · HD2 · MIP1.
Called loci 1
undetermined HD family · Basidiomycota
high confidence- core MAT gene
- conserved flank
- search hit only
- Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
- Location
- PchrRP-78_
SC013: · 13.5 kb1,063,437–1,076,948 - Own genes
- PchrRP-78_
SC013: · 13.5 kb1,063,437–1,076,948 - Locus
- Complete locus: MAT gene(s) with their flanking genes.
- Genes modelled
- 4 of 4 gene hits
- Nearest contig end
- 158.7 kb
- Region (samtools)
PchrRP-78_SC013:1063437-1076948
Gene evidence
| Gene | Role | Model | Identity % | E-value | Position (strand) | Exons | Reference record | FungiDB gene |
|---|---|---|---|---|---|---|---|---|
| beta_fg | conserved flank | hit onlyDIAMOND, proteome | 56.7cov 76.4% | 6.7e-49155 bits | 1,063,437–1,064,779 + | – | 192523_ | AGR57_12112 |
| HD1 | core MAT | hit onlyDIAMOND, proteome | 40.9cov 48.5% | 7.1e-61206 bits | 1,070,153–1,072,196 - | – | 2822231_ | AGR57_12117 |
| HD2 | core MAT | hit onlyDIAMOND, proteome | 37.4cov 66.4% | 1.8e-62204 bits | 1,072,398–1,074,098 + | – | 2822231_ | AGR57_12118 |
| MIP1 | conserved flank | hit onlyDIAMOND, proteome | 84.6cov 98.4% | < 1e-180989 bits | 1,074,457–1,076,948 - | – | 2822231_ | AGR57_12119 |
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:HD, Basidiomycota:PR
- Genetic code
- 1
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
Families searched but not called
| family | reason | best % of genes found | genes found |
|---|---|---|---|
| Basidiomycota:PR | best cluster carried 0 modelled gene(s), below the 2 required to report a locus; none of its genes could be modelled | 50.0 | pheromone_B44, fungal_mating_type_pheromone |
Pheromone-receptor arrays
Receptor arrays occur for both mating and non-mating STE3-like receptors (the study found arrays holding paralogs beside the mating receptors in Coprinopsis cinerea and Schizophyllum commune), so array membership does not establish that a locus is a mating receptor. receptor_array_support is a flag on the evidence behind an array; it never changes a call, its confidence or its verification label. receptor_cassette_* fields describe pheromone-precursor cassette structure (2 or more strict-CAAX ORFs within 5 kb of a receptor locus; class C when that many of those ORFs also carry tblastn precursor homology). They are descriptive only: the CAAX scan is also what admits a PR call, so cassettes are circular as confirmation; own-species curated precursors are a self-hit for class C; tandem receptors may be merged into one locus. They never change a call, tier, label, confidence or count.
| array | location | loci | calls | support | reasons |
|---|---|---|---|---|---|
| Basidiomycota:PR:PchrRP-78_SC005:948455-950020 | PchrRP-78_ | 1 | 0 | unsupported | a single receptor locus; no pheromone-precursor homology hit; 0 strict-CAAX pheromone ORFs |
| Basidiomycota:PR:PchrRP-78_SC009:1117669-1128912 | PchrRP-78_ | 3 | 0 | supported | array of 2 or more receptor loci |
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 (3); fewer than 2 genes could be modelled (2).
Show the 5 withheld loci
Withheld loci (5)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| PR | PchrRP-78_ | undetermined | pheromone_B44, fungal_mating_type_pheromone | 0 | fewer than 2 genes could be modelled |
| PR | PchrRP-78_ | undetermined | pheromone_B44, fungal_mating_type_pheromone | 0 | fewer than 2 genes could be modelled |
| PR | PchrRP-78_ | undetermined | pheromone_receptor | 1 | too few of the family's genes found |
| PR | PchrRP-78_ | undetermined | pheromone_receptor | 1 | too few of the family's genes found |
| PR | PchrRP-78_ | undetermined | pheromone_receptor | 1 | too few of the family's genes found |
Provenance
- Genome file
- PchrysosporiumRP-78.genome.fasta
- Assembly
- 232 contigs · 35.1 Mb · N50 1.9 Mb
- Genome SHA-256
- ec093f93b4b69498c4b3860cf8fdc6a0a7e2c03f71e8175bc5a3b30a458cfe19
- 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': 396331, 'routing_taxid_rank': 'family', 'flags': ['high_N'], '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 396331', 'routed_by': 'family taxid 396331 (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
- 2026-11-07T01:54:51Z
- Run time
- 59 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.