MATPredict · mating-type report

SchartarumIBT40293

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 02:37 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 KL651303MAT1-2 locus: genes from left to right on KL651303, 65,469 to 82,569: SLA2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).65 kb70 kb75 kb80 kb← 64.6 kb more to contig endcalled locusSLA2: conserved flank, 65,469–69,118 (+), identity 82.2%, search hit onlySLA2MAT1-1-3: core MAT gene, 77,568–78,432 (+), identity 33.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 77,568–78,432 (+), identity 52.9%, search hit onlyMAT1-2-1APN2: conserved flank, 79,016–81,205 (-), identity 86.4%, search hit onlyAPN2COX13: conserved flank, 81,879–82,569 (+), identity 66.2%, search hit onlyCOX13
Gene order on KL651303. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on KL651303, 64,613 to 83,425S40293_06324 65,469-69,118 (+): ANTH domain | I/LWEQ domain | domain-containing proteinS40293_06324S40293_11063 74,315-76,108 (-): unspecified productS40293_11063S40293_06325 77,568-78,432 (+): HMG (high mobility group) box | domain-containing proteinS40293_06325S40293_06326 79,016-81,205 (-): DNA-(apurinic or apyrimidinic site) endonuclease 2S40293_06326S40293_06327 81,879-82,569 (+): Cytochrome c oxidase subunit VIa | domain-containing proteinS40293_06327S40293_06328 83,259-85,728 (+): Anaphase-promoting complex subunit 5 | domain-containing proteinS40293_06328
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
KL651303:65,469–82,569 · 17.1 kb
Own genes
KL651303:65,469–82,569 · 17.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
65.5 kb
Region (samtools)
KL651303:65469-82569
Idiomorph scores
  • MAT1-2 132.0

Margin over the set-aside MAT1-1-3 hit: 19.6 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
MAT1-2-152.9MAT1-1-333.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome82.2cov 100.0%< 1e-1801,441 bits65,469–69,118 +–27337_vdls-17_MAT_MAT1-2S40293_06324
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome33.3cov 41.7%2.7e-1051 bits77,568–78,432 +–230073_uamh-1363_MAT_MAT1-1S40293_06325
MAT1-2-1core MAThit onlyDIAMOND, proteome52.9cov 81.0%1.7e-40132 bits77,568–78,432 +–61372_suf959_MAT_MAT1-2S40293_06325
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%1.3e-219615 bits79,016–81,205 -–2903220_liq80xsp_MAT_combinedS40293_06326
COX13conserved flankhit onlyDIAMOND, proteome66.2cov 100.0%1.0e-64186 bits81,879–82,569 +–578113_sxlc146_MAT_MAT1-2S40293_06327

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
MATKL651248:37,220–38,615MAT1-2MAT1-2-11too few of the family's genes found
MATKL651680:24,977–31,977MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
SchartarumIBT40293.genome.fasta
Assembly
2,342 contigs · 36.5 Mb · N50 200.0 kb
Genome SHA-256
a8475dc46a8a8c2b9a2eff74b203c87717a63f316e230f6bbc7a7cfd1b8043c6
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': 'genus', 'routing_taxid': 1667166, '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 1667166', 'routed_by': 'family taxid 1667166 (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
2026-11-07T02:35:29Z
Run time
93 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