MATPredict · mating-type report

TreeseiQM6a2017

MAT locus above the FungiDB annotation (gene by gene)

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 03:01 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on CP016234.1MAT1-2 locus: genes from left to right on CP016234.1, 3,881,347 to 3,894,174: SLA2 (conserved flank, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-4 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand).3,885 kb3,890 kb1,416.6 kb more to contig end →called locusSLA2: conserved flank, 3,881,347–3,884,830 (+), identity 81.6%, search hit onlySLA2COX13: conserved flank, 3,888,365–3,889,110 (-), identity 65.9%, search hit onlyCOX13APN2: conserved flank, 3,889,614–3,892,018 (+), identity 86.4%, search hit onlyAPN2MAT1-2-4: core MAT gene, 3,891,458–3,891,745 (+), identity 26.263%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 3,893,340–3,894,174 (-), identity 37.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 3,893,340–3,894,174 (-), identity 64.0%, search hit onlyMAT1-2-1
Gene order on CP016234.1. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CP016234.1, 3,880,707 to 3,894,814TrQ_004966 3,881,086-3,885,763 (+): ANTH domain | I/LWEQ domain | domain-containing proteinTrQ_004966TrQ_004967 3,885,041-3,887,617 (-): Anaphase-promoting complex subunit 5 | domain-containing proteinTrQ_004967TrQ_004969 3,888,238-3,892,711 (+): Endonuclease/Exonuclease/phosphatase family | domain-containing proteinTrQ_004969TrQ_004968 3,888,365-3,889,110 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinTrQ_004968TrQ_004970 3,892,652-3,894,404 (-): HMG (high mobility group) box | domain-containing proteinTrQ_004970
FungiDB release 71 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • 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
CP016234.1:3,881,347–3,894,174 · 12.8 kb
Own genes
CP016234.1:3,881,347–3,894,174 · 12.8 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
1.4 Mb
Region (samtools)
CP016234.1:3881347-3894174
Idiomorph scores
  • MAT1-2 148.0

Margin over the set-aside MAT1-1-3 hit: 26.7 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
MAT1-2-164.0MAT1-1-337.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,449 bits3,881,347–3,884,830 +–107463_unknown-1_MAT_MAT1-2TrQ_004966
COX13conserved flankhit onlyDIAMOND, proteome65.9cov 99.2%6.4e-61176 bits3,888,365–3,889,110 -–578113_sxlc146_MAT_MAT1-2TrQ_004969 (opposite strand)
TrQ_004968
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%1.2e-221624 bits3,889,614–3,892,018 +–2903220_liq80xsp_MAT_combinedTrQ_004969
MAT1-2-4core MAThit onlytblastn26.3cov 38.0%7.7e+0028 bits3,891,458–3,891,745 +–746128_af293_MAT_MAT1-2TrQ_004969
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome37.3cov 41.7%2.0e-1154 bits3,893,340–3,894,174 -–230073_uamh-1363_MAT_MAT1-1TrQ_004970
MAT1-2-1core MAThit onlyDIAMOND, proteome64.0cov 68.3%1.3e-46148 bits3,893,340–3,894,174 -–61372_suf959_MAT_MAT1-2TrQ_004970

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)

familylocationidiomorph genesmodelledreason
MATCP016232.1:3,348,807–3,350,242MAT1-2MAT1-2-11too few of the family's genes found
MATCP016236.1:3,348,854–3,349,516MAT1-1MAT1-1-31too few of the family's genes found

Provenance

Genome file
TreeseiQM6a2017.genome.fasta
Assembly
7 contigs · 34.9 Mb · N50 5.3 Mb
Genome SHA-256
2583d98f2ff543df0e4dc2c108e4bf99fdfc3299bea43af8d5b8179bd560b647
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': 5129, '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 5129', 'routed_by': 'family taxid 5129 (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
2026-11-07T03:00:11Z
Run time
105 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