Result
Mating type
- MAT1-2: locus, medium confidence, 12.6 kb on JAJJXM010000056. Gene order: MAT1-2-1 · APN2.
Called loci 1
MAT1-2 MATtub family · Ascomycota
medium confidence- core MAT gene
- conserved flank
- search hit only
- Location
- JAJJXM010000056:
335,693–348,245 · 12.6 kb - Own genes
- JAJJXM010000056:
335,693–348,245 · 12.6 kb - Locus
- Provisional: the call only tied the admission bar, or came from the relaxed pass.
- Genes modelled
- 2 of 2 gene hits
- Nearest contig end
- 103.9 kb
- Region (samtools)
JAJJXM010000056:335693-348245- Detection pass
- relaxed
Idiomorph scores
- MAT1-2 82.4
No other idiomorph scored.
Score: bitscore of the best core-gene hit for each idiomorph.
Gene evidence
| Gene | Role | Model | Identity % | E-value | Position (strand) | Exons | Reference record | FungiDB gene |
|---|---|---|---|---|---|---|---|---|
| MAT1-2-1 | core MAT | hit onlyDIAMOND, proteome | 45.3cov 53.4% | 1.3e-2182 bits | 335,693–336,672 - | – | 55307_ | BZA77DRAFT_323747 |
| APN2 | conserved flank | hit onlyDIAMOND, proteome | 68.8cov 89.2% | 1.3e-126363 bits | 346,192–348,245 - | – | 1174673_ | BZA77DRAFT_286141 |
| Rsm22-like | expected, not found | – | ||||||
| unnamed_flanking_ORF | expected, not found | – | ||||||
What was searched
- Routing
- By taxonomy. The genome's taxonomy falls inside a curated family's scope; only those families were searched.
- Families searched
- Ascomycota:MATtub
- Genetic code
- 1
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
Withheld candidate loci 4
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 (1).
Show the 4 withheld loci
Withheld loci (4)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| MATtub | JAJJXM010000006: | MAT1-2 | MAT1-1-1, MAT1-2-1 | 0 | fewer than 2 genes could be modelled |
| MATtub | JAJJXM010000012: | MAT1-2 | MAT1-2-1 | 1 | too few of the family's genes found |
| MATtub | JAJJXM010000033: | undetermined | SLA2 | 1 | too few of the family's genes found |
| MATtub | JAJJXM010000064: | undetermined | Rsm22-like | 1 | too few of the family's genes found |
Provenance
- Genome file
- PomphalodesCBS100304.genome.fasta
- Assembly
- 260 contigs · 61.0 Mb · N50 709.5 kb
- Genome SHA-256
- 33ebdb49d96e50fca85f5f05e7e00298c8cd26edbf407ad41804927c5e354a24
- 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': 110846, '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 110846', 'routed_by': 'family taxid 110846 (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
- 2026-11-07T01:51:53Z
- Run time
- 46 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.