MATPredict · mating-type report

CneoformansH992018

organism not recorded

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 01:57 UTC by MATPredict 0.8.1

Result

Mating type

alphahigh confidence

Called loci 1

alpha MAT family · Basidiomycota

high confidence
Gene order of the alpha locus on NPNB01000010alpha locus: genes from left to right on NPNB01000010, 183,859 to 286,717: FAO1 (conserved flank, plus strand); SXI1 (core MAT gene, plus strand); STE3 (core MAT gene, minus strand); MFa (core MAT gene, minus strand); MFalpha (core MAT gene, minus strand); RPL39 (core MAT gene, plus strand); PAN6 (conserved flank, plus strand).180 kb200 kb220 kb240 kb260 kb280 kb← 178.7 kb more to contig endcalled locusFAO1: conserved flank, 183,859–185,215 (+), identity 94.33%, gene modelFAO1SXI1: core MAT gene, 185,988–187,346 (+), identity 83.17%, gene modelSXI1STE3: core MAT gene, 208,377–209,695 (-), identity 94.69%, gene modelSTE3MFa: core MAT gene, 222,503–222,616 (-), identity 52.381%, search hit onlyMFa (lost to MFalpha)MFalpha: core MAT gene, 222,503–222,616 (-), identity 86.84%, gene modelMFalphaRPL39: core MAT gene, 270,789–271,045 (+), identity 92.16%, gene modelRPL39PAN6: conserved flank, 284,943–286,717 (+), identity 92.16%, gene modelPAN6
Gene order on NPNB01000010. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • search hit only
Location
NPNB01000010:183,859–286,717 · 102.9 kb
Own genes
NPNB01000010:183,859–286,717 · 102.9 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
183.9 kb
Region (samtools)
NPNB01000010:183859-286717
Idiomorph scores
  • alpha 594.0

Margin over the set-aside MFa hit: 34.5 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.

keptidentity %set asideidentity %overlap %basis
MFalpha86.8MFa52.4100.0higher identity
MFalpha86.8MFa52.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
FAO1conserved flankgene modelexonerate94.3cov 100.0%3.2e-168357 bits183,859–185,215 +640410_jec20_MAT_a
SXI1core MATgene modelexonerate83.2cov 100.0%< 1e-180594 bits185,988–187,346 +340410_jec21_MAT_alpha
STE3core MATgene modelexonerate94.7cov 100.0%< 1e-180548 bits208,377–209,695 -440410_jec21_MAT_alpha
MFacore MATlost to MFalpha, not countedhit onlytblastn52.4cov 100.0%1.1e-0127 bits222,503–222,616 -–40410_jec20_MAT_a
MFalphacore MATgene modelexonerate86.8cov 100.0%1.9e-1257 bits222,503–222,616 -140410_jec21_MAT_alpha
RPL39core MATgene modelexonerate92.2cov 100.0%1.2e-1667 bits270,789–271,045 +240410_jec20_MAT_a
PAN6conserved flankgene modelexonerate92.2cov 100.0%1.2e-172307 bits284,943–286,717 +740410_jec20_MAT_a
NOG2not searchable: no reference protein in the database
UAP1not searchable: no reference protein in the database

Withheld candidate loci 3

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).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATNPNB01000006:278,370–422,938aSTE3, SXI20fewer than 2 genes could be modelled
MATNPNB01000012:820,042–908,998alphaMFalpha, STE30fewer than 2 genes could be modelled
MATNPNB01000014:1,950,250–2,020,401undeterminedPAN6, STE30fewer than 2 genes could be modelled

Provenance

Genome file
CneoformansH992018.genome.fasta
Assembly
14 contigs · 18.9 Mb · N50 1.4 Mb
Genome SHA-256
49700fd3756e2762c0bfad17d5696102aaeaf0b71c756bbde7feb9119a65ecc6
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': 1884633, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 1884633', 'routed_by': 'family taxid 1884633 (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
2026-11-07T01:57:35Z
Run time
23 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