MATPredict · mating-type report

CgraminicolaM1-001

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 02:27 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 GG697345MAT1-2 locus: genes from left to right on GG697345, 256,537 to 273,073: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); SLA2 (conserved flank, minus strand).260 kb265 kb270 kb← 255.7 kb more to contig endcalled locusCOX13: conserved flank, 256,537–257,378 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 258,012–260,302 (+), identity 84.1%, search hit onlyAPN2MAT1-1-3: core MAT gene, 260,650–261,489 (-), identity 32.4%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 260,650–261,489 (-), identity 51.3%, search hit onlyMAT1-2-1SLA2: conserved flank, 269,590–273,073 (-), identity 82.9%, search hit onlySLA2
Gene order on GG697345. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on GG697345, 255,710 to 273,899GLRG_04640 253,788-256,269 (+): anaphase-promoting complex proteinGLRG_04640GLRG_04641 256,537-257,378 (-): cytochrome c oxidase subunit VIaGLRG_04641GLRG_04642 258,012-260,302 (+): endonuclease/Exonuclease/phosphataseGLRG_04642GLRG_04643 260,650-261,489 (-): HMG box proteinGLRG_04643GLRG_04644 269,590-273,073 (-): ANTH domain-containing proteinGLRG_04644
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
GG697345:256,537–273,073 · 16.5 kb
Own genes
GG697345:256,537–273,073 · 16.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
256.5 kb
Region (samtools)
GG697345:256537-273073
Idiomorph scores
  • MAT1-2 145.0

Margin over the set-aside MAT1-1-3 hit: 18.9 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
MAT1-2-151.3MAT1-1-332.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 72.5%5.3e-62179 bits256,537–257,378 -–5158_cbs114723_MAT_unswitchedGLRG_04641
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%2.7e-210592 bits258,012–260,302 +–2903220_liq80xsp_MAT_combinedGLRG_04642
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome32.4cov 41.1%3.1e-1050 bits260,650–261,489 -–230073_uamh-1363_MAT_MAT1-1GLRG_04643
MAT1-2-1core MAThit onlyDIAMOND, proteome51.3cov 24.8%1.3e-45145 bits260,650–261,489 -–746128_af293_MAT_MAT1-2GLRG_04643
SLA2conserved flankhit onlyDIAMOND, proteome82.9cov 100.0%< 1e-1801,489 bits269,590–273,073 -–27337_vdls-17_MAT_MAT1-2GLRG_04644

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
MATGG697342:54,884–56,373MAT1-2MAT1-2-11too few of the family's genes found
MATGG697370:113,386–115,585MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CgraminicolaM1-001.genome.fasta
Assembly
654 contigs · 51.6 Mb · N50 579.2 kb
Genome SHA-256
b22a2124172e40a0eb67d6b2a9c52f89ae787077d0057b5afaa78f96592d0a6e
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': 681950, '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 681950', 'routed_by': 'family taxid 681950 (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
2026-11-07T02:26:07Z
Run time
109 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