Result
No MAT locus called
No family reached the evidence bar. That is weak evidence that the locus is absent: a fragmented assembly, or a lineage far from every reference, often explains it.
Next: check the withheld candidate loci below against a known locus, or type the strain from its reads.
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
Families searched but not called
| family | reason | best % of genes found | genes found |
|---|---|---|---|
| Ascomycota:MAT | best cluster was flank-carried -- no core gene could be modelled -- and its strongest core hit scores below 39 bits or lies outside the flank span (+-20000 bp) | 60.0 | APN2, SLA2, COX13 |
Withheld candidate loci 7
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: fewer than 2 genes could be modelled (3); too few of the family's genes found (3); MAT hit outside the flanking genes' span (1).
Show the 7 withheld loci
Withheld loci (7)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| MAT | JAKRRZ010000843: | undetermined | APN2, SLA2, COX13 | 3 | MAT hit outside the flanking genes' span |
| MAT | JAKRRZ010000866: | undetermined | MAT1-2-1, MAT1-1-2 | 0 | fewer than 2 genes could be modelled |
| MAT | JAKRRZ010000135: | MAT1-2 | MAT1-2-1, MAT1-1-3 | 0 | fewer than 2 genes could be modelled |
| MAT | JAKRRZ010000239: | MAT1-1 | MAT1-1-1, CIMG_00407 | 0 | fewer than 2 genes could be modelled |
| MAT | JAKRRZ010000352: | MAT1-2 | MAT1-2-1 | 1 | too few of the family's genes found |
| MAT | JAKRRZ010002827: | MAT1-1 | MAT1-1-1 | 1 | too few of the family's genes found |
| MAT | JAKRRZ010003763: | MAT1-2 | MAT1-2-1 | 1 | too few of the family's genes found |
Provenance
- Genome file
- PaphanisDRCT72020.genome.fasta
- Assembly
- 12,357 contigs · 55.6 Mb · N50 11.4 kb
- Genome SHA-256
- 031b8bb4f3183bd268c77381c7cbc95770e1b17621d28e1303f561fffa2cf4d9
- 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': 'genus', 'routing_taxid': 34371, '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 34371', 'routed_by': 'family taxid 34371 (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
- 2026-11-07T02:31:02Z
- Run time
- 102 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.
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.