Result
Mating type
- M: MAT gene without flanking genes, high confidence, 14.2 kb on CAKM01000262. Gene order: matPi · matMc · matMi.
Called loci 1
M PM family · Ascomycota
high confidence- core MAT gene
- gene model
- search hit only
- Location
- CAKM01000262:
47,080–61,327 · 14.2 kb - Cross-lineage class
- MAT1-2
- Own genes
- CAKM01000262:
47,080–57,517 · 10.4 kb · the span runs 3.8 kb beyond these genes - Locus
- A MAT gene with no flanking gene beside it; not a full locus.
- Genes modelled
- 3 of 3 gene hits
- Nearest contig end
- 30.3 kb
- Region (samtools)
CAKM01000262:47080-61327
Idiomorph scores
- M 519.0
- P 446.0
Margin over the next idiomorph: 73.0
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 |
|---|---|---|---|---|---|---|---|---|
| matPi | core MAT | hit onlyDIAMOND, proteome | 99.6cov 97.8% | 1.6e-165446 bits | 47,080–48,131 - | – | 42068_ | PNEJI1_000366 |
| matMc | core MAT | gene modelexonerate | 100.0cov 100.0% | 1.8e-170519 bits | 56,442–57,194 - | 1 | 42068_ | none |
| matMi | core MAT | gene modelexonerate | 98.6cov 100.0% | 1.9e-38132 bits | 57,308–57,517 + | 1 | 42068_ | none |
| matPc | 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
- Ascomycota:PM
- Genetic code
- 1
- Taxonomy
- local NCBI taxonomy snapshot 2026-10-01
Withheld candidate loci 10
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 (10).
Show the 10 withheld loci
Withheld loci (10)
| family | location | idiomorph | genes | modelled | reason |
|---|---|---|---|---|---|
| PM | CAKM01000002: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000141: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000229: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000236: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000279: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000006: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000258: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000157: | M | matMi | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000197: | M | matMc | 0 | fewer than 2 genes could be modelled |
| PM | CAKM01000220: | M | matMc | 0 | fewer than 2 genes could be modelled |
Provenance
- Genome file
- PjiroveciiSE8.genome.fasta
- Assembly
- 331 contigs · 8.1 Mb · N50 41.6 kb
- Genome SHA-256
- 09e4d2839a86b2a699b0adcb5a4702fe646208abdeefd16ba39bedce3564226f
- 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': 44281, 'routing_taxid_rank': 'family', 'flags': ['short_genome'], '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 44281', 'routed_by': 'family taxid 44281 (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
- 2026-11-07T02:48:08Z
- Run time
- 15 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.