MATPredict · mating-type report

HmississippienseNAm1

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 02:35 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 CH476655MAT1-1 locus: genes from left to right on CH476655, 4,108,229 to 4,126,313: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand).4,110 kb4,115 kb4,120 kb4,125 kb3,216.1 kb more to contig end →called locusSLA2: conserved flank, 4,108,229–4,112,522 (+), identity 90.7%, search hit onlySLA2MAT1-1-1: core MAT gene, 4,115,993–4,116,469 (-), identity 66.7%, search hit onlyMAT1-1-1MAT1-1-4: core MAT gene, 4,118,242–4,119,121 (-), identity 47.2%, search hit onlyMAT1-1-4COX13: conserved flank, 4,122,183–4,122,890 (-), identity 70.3%, search hit onlyCOX13APN2: conserved flank, 4,123,278–4,126,313 (+), identity 84.1%, search hit onlyAPN2
Gene order on CH476655. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CH476655, 4,107,324 to 4,127,218HCAG_01167 4,108,229-4,112,522 (+): ANTH domain | I/LWEQ domain | domain-containing proteinHCAG_01167HCAG_01168 4,115,993-4,116,469 (-): predicted proteinHCAG_01168HCAG_01169 4,116,816-4,117,215 (-): predicted proteinHCAG_01169HCAG_01170 4,118,242-4,119,121 (-): predicted proteinHCAG_01170HCAG_01171 4,120,854-4,121,384 (-): predicted proteinHCAG_01171HCAG_01172 4,122,183-4,122,890 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinHCAG_01172HCAG_01173 4,123,278-4,126,313 (+): DNA-(apurinic or apyrimidinic site) endonuclease 2HCAG_01173HCAG_01174 4,126,842-4,133,292 (+): Transcription mediator complex subunit Med12 | SRB8 ARM-like domain | domain-containing proteinHCAG_01174
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
Location
CH476655:4,108,229–4,126,313 · 18.1 kb
Own genes
CH476655:4,108,229–4,126,313 · 18.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
3.2 Mb
Region (samtools)
CH476655:4108229-4126313
Idiomorph scores
  • MAT1-1 109.0

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 recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome90.7cov 99.3%< 1e-1801,467 bits4,108,229–4,112,522 +–107463_unknown-1_MAT_MAT1-2HCAG_01167
MAT1-1-1core MAThit onlyDIAMOND, proteome66.7cov 14.7%1.1e-2388 bits4,115,993–4,116,469 -–199306_rmscc1040_MAT_MAT1-1HCAG_01168
MAT1-1-4core MAThit onlyDIAMOND, proteome47.2cov 48.4%3.8e-32109 bits4,118,242–4,119,121 -–199306_rmscc1040_MAT_MAT1-1HCAG_01170
COX13conserved flankhit onlyDIAMOND, proteome70.3cov 90.0%5.0e-50149 bits4,122,183–4,122,890 -–199306_rmscc1040_MAT_MAT1-1HCAG_01172
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%1.5e-159465 bits4,123,278–4,126,313 +–2903220_liq80xsp_MAT_combinedHCAG_01173

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATCH476655:5,820,043–5,822,283MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
HmississippienseNAm1.genome.fasta
Assembly
280 contigs · 33.0 Mb · N50 2.9 Mb
Genome SHA-256
100205a2e3886c5f9689b19c88a0c75f294320492c94fa2c2c714fd50366c439
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': 299071, '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 299071', 'routed_by': 'family taxid 299071 (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
2026-11-07T02:34:29Z
Run time
76 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