Result
Mating type
- MAT1-2: complete locus, high confidence, 16.8 kb on LTAN01000007. Gene order: SLA2 · MAT1-2-1 · APN2 · COX13.
Called loci 1
MAT1-2 MAT family · Ascomycota
high confidence- core MAT gene
- conserved flank
- search hit only
- MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
- Location
- LTAN01000007:
829,775–846,570 · 16.8 kb - Own genes
- LTAN01000007:
829,775–846,570 · 16.8 kb - Locus
- Complete locus: MAT gene(s) with their flanking genes.
- Genes modelled
- 4 of 5 gene hits
- Nearest contig end
- 829.8 kb
- Region (samtools)
LTAN01000007:829775-846570
Idiomorph scores
- MAT1-2 148.0
Margin over the set-aside MAT1-1-3 hit: 21.6 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 |
|---|---|---|---|---|---|
| MAT1-2-1 | 50.0 | MAT1-1-3 | 28.4 | 100.0 | higher identity |
Gene evidence
| Gene | Role | Model | Identity % | E-value | Position (strand) | Exons | Reference record | FungiDB gene |
|---|---|---|---|---|---|---|---|---|
| SLA2 | conserved flank | hit onlyDIAMOND, proteome | 85.2cov 100.0% | < 1e-1801,499 bits | 829,775–833,242 + | – | 27337_ | CH63R_09968 |
| MAT1-2-1 | core MAT | hit onlyDIAMOND, proteome | 50.0cov 18.6% | 1.3e-46148 bits | 841,428–842,285 + | – | 1873960_ | CH63R_09970 |
| MAT1-1-3 | core MATother idiomorph, not countedlost to MAT1-2-1, not counted | hit onlytblastn | 28.4cov 43.0% | 9.3e-0543 bits | 841,902–842,186 + | – | 230073_ | CH63R_09970 |
| APN2 | conserved flank | hit onlyDIAMOND, proteome | 81.8cov 36.7% | 7.7e-215601 bits | 842,569–844,574 - | – | 2903220_ | CH63R_09971 |
| COX13 | conserved flank | hit onlyDIAMOND, proteome | 70.8cov 72.5% | 4.6e-63182 bits | 845,703–846,570 + | – | 5158_ | CH63R_09972 |
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:MAT
- Genetic code
- 1
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
Withheld candidate loci 2
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 (2).
Show the 2 withheld loci
Withheld loci (2)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| MAT | CM004461: | MAT1-2 | MAT1-2-1 | 1 | too few of the family's genes found |
| MAT | CM004462: | MAT1-2 | MAT1-2-1 | 1 | too few of the family's genes found |
Provenance
- Genome file
- ChigginsianumIMI349063.genome.fasta
- Assembly
- 25 contigs · 50.7 Mb · N50 5.2 Mb
- Genome SHA-256
- 3fd01b7a68f12843fe6acb99a425f7a8011c1fdc51ce2e4e84d33dab85a7793c
- 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': 681950, '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 681950', 'routed_by': 'family taxid 681950 (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
- 2026-11-07T02:04:23Z
- Run time
- 111 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.