MATPredict · mating-type report

NgypseaCBS118893

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 02:42 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 DS989825MAT1-1 locus: genes from left to right on DS989825, 2,207,204 to 2,219,339: CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand); SLA2 (conserved flank, minus strand).2,208 kb2,210 kb2,212 kb2,214 kb2,216 kb2,218 kb797.4 kb more to contig end →called locusCIMG_00407: core MAT gene, 2,207,204–2,207,323 (-), identity 37.5%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 2,207,213–2,207,392 (-), identity 33.333%, search hit onlyMAT1-2-4MAT1-1-1: core MAT gene, 2,208,025–2,209,228 (-), identity 49.7%, search hit onlyMAT1-1-1MAT1-1-4: core MAT gene, 2,209,884–2,211,155 (-), identity 44.3%, search hit onlyMAT1-1-4APN2: conserved flank, 2,211,925–2,214,018 (-), identity 76.6%, search hit onlyAPN2COX13: conserved flank, 2,214,266–2,214,936 (+), identity 68.1%, search hit onlyCOX13SLA2: conserved flank, 2,215,362–2,219,339 (-), identity 88.1%, search hit onlySLA2
Gene order on DS989825. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on DS989825, 2,206,597 to 2,219,944MGYG_05518 2,207,001-2,207,943 (-): unspecified productMGYG_05518MGYG_05519 2,208,025-2,209,228 (-): alpha-box mating type proteinMGYG_05519MGYG_05520 2,209,884-2,211,155 (-): unspecified productMGYG_05520MGYG_05521 2,211,925-2,214,018 (-): DNA-(apurinic or apyrimidinic site) lyase 2MGYG_05521MGYG_05522 2,214,266-2,214,936 (+): Cox13pMGYG_05522MGYG_05523 2,215,362-2,219,339 (-): SLA2MGYG_05523MGYG_05524 2,219,888-2,222,591 (-): uncharacterized PH domain-containing proteinMGYG_05524
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
  • CIMG_00407 is a weak hit to the other idiomorph's gene and was not counted against the call.
  • MAT1-2-4 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
DS989825:2,207,204–2,219,339 · 12.1 kb
Own genes
DS989825:2,207,204–2,219,339 · 12.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
798.0 kb
Region (samtools)
DS989825:2207204-2219339
Idiomorph scores
  • MAT1-1 298.0
  • MAT1-2 42.0

Margin over the next idiomorph: 256.0

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
CIMG_00407core MATother idiomorph, not countedhit onlytblastn37.5cov 15.0%1.0e-0340 bits2,207,204–2,207,323 -–5501_rs_MAT_MAT1-2MGYG_05518
MAT1-2-4core MATother idiomorph, not countedhit onlytblastn33.3cov 24.0%1.8e-0442 bits2,207,213–2,207,392 -–746128_af293_MAT_MAT1-2MGYG_05518
MAT1-1-1core MAThit onlyDIAMOND, proteome49.7cov 98.7%3.8e-101298 bits2,208,025–2,209,228 -–199306_rmscc1040_MAT_MAT1-1MGYG_05519
MAT1-1-4core MAThit onlyDIAMOND, proteome44.3cov 68.7%7.4e-47150 bits2,209,884–2,211,155 -–199306_rmscc1040_MAT_MAT1-1MGYG_05520
APN2conserved flankhit onlyDIAMOND, proteome76.6cov 90.4%3.5e-237663 bits2,211,925–2,214,018 -–27339_unknown-1_MAT_MAT1-2MGYG_05521
COX13conserved flankhit onlyDIAMOND, proteome68.1cov 100.0%4.4e-59172 bits2,214,266–2,214,936 +–5501_rs_MAT_MAT1-2MGYG_05522
SLA2conserved flankhit onlyDIAMOND, proteome88.1cov 99.3%< 1e-1801,527 bits2,215,362–2,219,339 -–107463_unknown-1_MAT_MAT1-2MGYG_05523
MAT1-2-1expected, not found–

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
MATDS989826:200,037–200,555MAT1-1MAT1-1-11too few of the family's genes found
MATDS989827:727,421–748,246MAT1-2MAT1-2-1, MAT1-2-101too few of the family's genes found

Provenance

Genome file
NgypseaCBS118893.genome.fasta
Assembly
19 contigs · 23.3 Mb · N50 3.2 Mb
Genome SHA-256
4700369c50108fb2d0baf0efac9c3129e49e519b8fcfe5662be8cd73297b6c7c
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': 34384, '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 34384', 'routed_by': 'family taxid 34384 (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
2026-11-07T02:42:11Z
Run time
39 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