MATPredict · mating-type report

VgallopavaCBS43764

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 01:47 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 KN847532MAT1-2 locus: genes from left to right on KN847532, 1,005,911 to 1,031,087: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, plus strand).1,005 kb1,010 kb1,015 kb1,020 kb1,025 kb1,030 kb211.9 kb more to contig end →called locusCOX13: conserved flank, 1,005,911–1,006,457 (-), identity 54.7%, search hit onlyCOX13APN2: conserved flank, 1,006,767–1,008,804 (+), identity 86.4%, search hit onlyAPN2MAT1-1-4: core MAT gene, 1,009,604–1,009,765 (+), identity 29.63%, search hit onlyMAT1-1-4MAT1-2-1: core MAT gene, 1,011,049–1,011,426 (-), identity 55.77%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 1,011,145–1,011,429 (-), identity 31.579%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-1-1: core MAT gene, 1,011,220–1,011,414 (-), identity 33.333%, search hit onlyMAT1-1-1 (lost to MAT1-2-1)MAT1-1-2: core MAT gene, 1,030,989–1,031,087 (+), identity 33.333%, search hit onlyMAT1-1-2
Gene order on KN847532. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KN847532, 1,004,654 to 1,032,347PV09_01797 1,003,246-1,005,845 (+): Anaphase-promoting complex subunit 5 [Source:UniProtKB/TrEMBL;Acc:A0A0D2B9G4]PV09_01797PV09_01798 1,005,659-1,006,524 (-): Cytochrome c oxidase subunit [Source:UniProtKB/TrEMBL;Acc:A0A0D2AMZ3]PV09_01798PV09_01799 1,006,673-1,008,939 (+): Endo/exonuclease/phosphatase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0D1XYL5]PV09_01799PV09_01800 1,009,036-1,010,256 (+): unspecified productPV09_01800PV09_01801 1,012,212-1,012,909 (+): unspecified productPV09_01801PV09_01802 1,013,476-1,016,642 (+): SMP-LTD domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0D2AMZ7]PV09_01802PV09_01803 1,016,813-1,018,279 (-): unspecified productPV09_01803PV09_01804 1,019,083-1,020,843 (+): hypothetical protein, variantPV09_01804PV09_01805 1,020,975-1,021,855 (-): unspecified productPV09_01805PV09_01806 1,021,860-1,024,243 (-): Ubiquitinyl hydrolase 1 [Source:UniProtKB/TrEMBL;Acc:A0A0D2AN03]PV09_01806PV09_01807 1,024,478-1,025,991 (+): unspecified productPV09_01807PV09_01808 1,025,897-1,028,388 (-): COP9 signalosome complex subunit 2 [Source:UniProtKB/TrEMBL;Acc:A0A0D1Z4K1]PV09_01808PV09_01809 1,028,807-1,030,834 (+): unspecified productPV09_01809PV09_01810 1,030,607-1,031,746 (-): unspecified productPV09_01810PV09_01811 1,031,843-1,032,910 (+): S4 RNA-binding domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A0D1XYN7]PV09_01811
FungiDB release 68 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
  • tools disagree
  • alternate model
  • search hit only
  • MAT1-1-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-1-2 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-1-4 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
KN847532:1,005,911–1,031,087 · 25.2 kb
Own genes
KN847532:1,005,911–1,031,087 · 25.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 7 gene hits
Nearest contig end
213.2 kb
Region (samtools)
KN847532:1005911-1031087
Idiomorph scores
  • MAT1-2 110.0
  • MAT1-1 33.9

Margin over the next idiomorph: 76.1

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
MAT1-2-144.9MAT1-1-133.3100.0higher identity
MAT1-2-144.9MAT1-1-331.698.9higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome54.7cov 94.8%4.7e-47142 bits1,005,911–1,006,457 -–5501_rs_MAT_MAT1-2PV09_01798
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%3.4e-210593 bits1,006,767–1,008,804 +–2903220_liq80xsp_MAT_combinedPV09_01799
MAT1-1-4core MATother idiomorph, not countedhit onlytblastn29.6cov 21.0%8.8e-0234 bits1,009,604–1,009,765 +–199306_rmscc1040_MAT_MAT1-1PV09_01800
MAT1-2-1core MATmodels differexonerateminiprot: 1,011,049–1,011,726, 37.4%55.8cov 29.9%2.6e-26110 bits1,011,049–1,011,426 -2115814_voucher-101_MAT_MAT1-2none
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn31.6cov 41.0%3.0e-0749 bits1,011,145–1,011,429 -–5518_3639_MAT_combinednone
MAT1-1-1core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn33.3cov 17.0%6.1e+0029 bits1,011,220–1,011,414 -–162425_fgsc-a4_MAT_combinednone
MAT1-1-2core MATother idiomorph, not countedhit onlytblastn33.3cov 9.0%6.9e+0029 bits1,030,989–1,031,087 +–5158_cbs114723_MAT_unswitchedPV09_01810 (opposite strand)
MAT1-1-1expected, not found–
SLA2expected, not found–

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: too few of the family's genes found (2); fewer than 2 genes could be modelled (1).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATKN847532:947,905–962,111MAT1-1MAT1-1-1, SLA21fewer than 2 genes could be modelled
MATKN847535:940,949–949,220MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATKN847557:35,078–37,419MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
VgallopavaCBS43764.genome.fasta
Assembly
367 contigs · 31.8 Mb · N50 572.0 kb
Genome SHA-256
56ffb4013f2e6dd2f1ccb98b2bf35d76447db84290881629fa8e60c35861f9e6
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': 1111112, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 1111112', 'routed_by': 'family taxid 1111112 (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
2026-11-07T01:47:04Z
Run time
52 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