MATPredict · mating-type report

FgraminearumPH-1

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 02:22 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 HG970333MAT1-1 locus: genes from left to right on HG970333, 3,004,628 to 3,024,863: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); MAT1-2-7 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, minus strand); SLA2 (conserved flank, minus strand).3,005 kb3,010 kb3,015 kb3,020 kb3,025 kb← 3,003.6 kb more to contig endcalled locusCOX13: conserved flank, 3,004,628–3,005,397 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 3,005,911–3,008,142 (+), identity 84.1%, search hit onlyAPN2MAT1-1-3: core MAT gene, 3,008,846–3,009,585 (-), identity 99.4%, search hit onlyMAT1-1-3MAT1-1-2: core MAT gene, 3,010,042–3,011,636 (+), identity 91.0%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 3,012,302–3,013,392 (+), identity 100.0%, search hit onlyMAT1-1-1MAT1-2-7: core MAT gene, 3,012,559–3,012,774 (+), identity 28.205%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)MAT1-2-1: core MAT gene, 3,014,004–3,014,868 (-), identity 99.6%, search hit onlyMAT1-2-1SLA2: conserved flank, 3,021,305–3,024,863 (-), identity 80.9%, search hit onlySLA2
Gene order on HG970333. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on HG970333, 3,003,616 to 3,025,874FGRAMPH1_01G11091 3,001,167-3,003,625 (-): anaphase-promoting complex subunit 5FGRAMPH1_01G11091FGRAMPH1_01G11093 3,004,628-3,005,397 (-): cytochrome c oxidase subunit 6aFGRAMPH1_01G11093FGRAMPH1_01G11095 3,005,911-3,008,142 (+): ap endonuclease 2FGRAMPH1_01G11095 APN2FGRAMPH1_01G11097 3,008,846-3,009,585 (-): mating type 1-1-3FGRAMPH1_01G11097 MAT1-1-3FGRAMPH1_01G11099 3,009,904-3,011,705 (+): mating type 1-1-2FGRAMPH1_01G11099FGRAMPH1_01G11101 3,012,208-3,013,392 (+): mating-type protein MAT-1FGRAMPH1_01G11101 MAT1-1-1FGRAMPH1_01G11103 3,013,642-3,014,974 (-): mating type 1-2-1FGRAMPH1_01G11103 MAT1-2-1FGRAMPH1_01G11105 3,015,616-3,016,448 (-): mating-type MAT-1FGRAMPH1_01G11105FGRAMPH1_01G11107 3,020,457-3,020,838 (+): unnamed protein productFGRAMPH1_01G11107FGRAMPH1_01G11109 3,020,797-3,025,198 (-): probable cytoskeleton assembly control SLA2FGRAMPH1_01G11109
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
HG970333:3,004,628–3,024,863 · 20.2 kb
Own genes
HG970333:3,004,628–3,024,863 · 20.2 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
7 of 8 gene hits
Nearest contig end
3.0 Mb
Region (samtools)
HG970333:3004628-3024863
Idiomorph scores
  • MAT1-1 771.0
  • MAT1-2 505.0

Margin over the next idiomorph: 266.0

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
MAT1-1-1100.0MAT1-2-728.2100.0higher identity
MAT1-2-199.6MAT1-1-338.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%3.1e-63182 bits3,004,628–3,005,397 -–578113_sxlc146_MAT_MAT1-2FGRAMPH1_01G11093
APN2conserved flankhit onlyDIAMOND, proteome84.1cov 36.7%6.6e-230645 bits3,005,911–3,008,142 +–2903220_liq80xsp_MAT_combinedFGRAMPH1_01G11095 APN2
MAT1-1-3core MAThit onlyDIAMOND, proteome99.4cov 100.0%1.3e-135370 bits3,008,846–3,009,585 -–5518_3639_MAT_combinedFGRAMPH1_01G11097 MAT1-1-3
MAT1-1-2core MAThit onlyDIAMOND, proteome91.0cov 87.5%2.5e-285771 bits3,010,042–3,011,636 +–5518_3639_MAT_combinedFGRAMPH1_01G11099
MAT1-1-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.4e-263706 bits3,012,302–3,013,392 +–5518_3639_MAT_combinedFGRAMPH1_01G11101 MAT1-1-1
MAT1-2-7core MATlost to MAT1-1-1, not countedhit onlytblastn28.2cov 39.0%6.2e-0234 bits3,012,559–3,012,774 +–5158_cbs114723_MAT_unswitchedFGRAMPH1_01G11101 MAT1-1-1
MAT1-2-1core MAThit onlyDIAMOND, proteome99.6cov 100.0%5.0e-187505 bits3,014,004–3,014,868 -–5518_3639_MAT_combinedFGRAMPH1_01G11103 MAT1-2-1
SLA2conserved flankhit onlyDIAMOND, proteome80.9cov 100.0%< 1e-1801,397 bits3,021,305–3,024,863 -–107463_unknown-1_MAT_MAT1-2FGRAMPH1_01G11109

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
MATHG970332:4,532,153–4,568,947MAT1-2MAT1-1-1, MAT1-2-1, MAT1-1-51too few of the family's genes found
MATHG970334:1,304,588–1,319,420MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found

Provenance

Genome file
FgraminearumPH-1.genome.fasta
Assembly
6 contigs · 38.0 Mb · N50 9.4 Mb
Genome SHA-256
7cc6849e195214481acb49d829807c94795115bc5ea97fd1132b08433fded879
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': 110618, '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 110618', 'routed_by': 'family taxid 110618 (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
2026-11-07T02:21:31Z
Run time
84 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