MATPredict · mating-type report

CposadasiiCPA0001

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 02:01 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on DS544497.1MAT1-1 locus: genes from left to right on DS544497.1, 374,986 to 387,647: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).376 kb378 kb380 kb382 kb384 kb386 kb388 kb98.1 kb more to contig end →called locusCOX13: conserved flank, 374,986–375,505 (-), identity 100.0%, the two modelling tools disagreeCOX13APN2: conserved flank, 375,844–377,929 (+), identity 100.0%, the two modelling tools disagreeAPN2MAT1-1-4: core MAT gene, 378,721–379,755 (+), identity 97.51%, the two modelling tools disagreeMAT1-1-4MAT1-1-1: core MAT gene, 380,356–381,143 (+), identity 88.33%, the two modelling tools disagreeMAT1-1-1SLA2: conserved flank, 383,708–387,647 (-), identity 97.81%, gene modelSLA2
Gene order on DS544497.1. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
Location
DS544497.1:374,986–387,647 · 12.7 kb
Own genes
DS544497.1:374,986–387,647 · 12.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
98.8 kb
Region (samtools)
DS544497.1:374986-387647
Idiomorph scores
  • MAT1-1 351.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankmodels differexonerateminiprot: 374,809–375,505, 99.8%1 frameshiftdefective gene model100.0cov 100.0%1.5e-62138 bits374,986–375,505 -35501_h538-4_MAT_MAT1-1
APN2conserved flankmodels differexonerateminiprot: 375,844–377,932, 97.0%100.0cov 100.0%< 1e-1801,109 bits375,844–377,929 +6199306_rmscc1040_MAT_MAT1-1
MAT1-1-4core MATmodels differexonerateminiprot: 378,721–379,758, 95.1%1 frameshiftdefective gene model97.5cov 100.0%2.4e-111351 bits378,721–379,755 +6199306_rmscc1040_MAT_MAT1-1
MAT1-1-1core MATmodels differexonerateminiprot: 380,356–381,604, 92.1%1 internal stopdefective gene model88.3cov 63.0%1.0e-137293 bits380,356–381,143 +2199306_rmscc1040_MAT_MAT1-1
SLA2conserved flankgene modelexonerate3 frameshiftsdefective gene model97.8cov 100.0%< 1e-180768 bits383,708–387,647 -125501_rs_MAT_MAT1-2

Withheld candidate loci 8

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 (8).

Show the 8 withheld loci

Withheld loci (8)

familylocationidiomorph genesmodelledreason
MATDS544512.1:97,549–111,320MAT1-2MAT1-2-1, SLA2, MAT1-2-100fewer than 2 genes could be modelled
MATDS544660.1:15,938–32,583MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS544534.1:40,035–50,845MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS544537.1:104,975–123,326MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATDS544502.1:123,282–138,167MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATDS544504.1:202,765–251,269MAT1-2MAT1-2-1, APN2, SLA2, MAT1-2-40fewer than 2 genes could be modelled
MATDS544498.1:124,427–140,432MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS544513.1:97,008–121,385MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled

Provenance

Genome file
CposadasiiCPA0001.genome.fasta
Assembly
256 contigs · 28.7 Mb · N50 210.5 kb
Genome SHA-256
58dbefde838eb187991dec720cc7008d70419eeca041367c2c67585dcc923357
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': 33184, 'routing_taxid_rank': 'family', 'flags': ['high_N'], '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 33184', 'routed_by': 'family taxid 33184 (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
2026-11-07T02:00:52Z
Run time
60 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