MATPredict · mating-type report

Foxysporum26406

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 02:00 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 JH659339.1MAT1-2 locus: genes from left to right on JH659339.1, 1,004,192 to 1,019,509: 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); MAT1-1-5 (core MAT gene, plus strand).1,005 kb1,010 kb1,015 kb1,020 kb276.9 kb more to contig end →called locusCOX13: conserved flank, 1,004,192–1,004,953 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 1,005,474–1,007,706 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 1,008,257–1,009,031 (-), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,008,257–1,009,031 (-), identity 100.0%, search hit onlyMAT1-2-1SLA2: conserved flank, 1,012,777–1,016,344 (-), identity 81.6%, search hit onlySLA2MAT1-1-5: core MAT gene, 1,019,378–1,019,509 (+), identity 37.5%, search hit onlyMAT1-1-5
Gene order on JH659339.1. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on JH659339.1, 1,003,427 to 1,020,274FOMG_13077 999,618-1,003,781 (-): anaphase-promoting complex subunit 5FOMG_13077FOMG_13078 1,003,876-1,005,046 (-): cytochrome c oxidase subunit 6aFOMG_13078FOMG_13079 1,005,164-1,007,895 (+): AP endonuclease 2FOMG_13079FOMG_13080 1,007,929-1,008,227 (-): hypothetical proteinFOMG_13080FOMG_13081 1,008,257-1,009,031 (-): hypothetical proteinFOMG_13081FOMG_13082 1,009,384-1,009,497 (+): hypothetical proteinFOMG_13082FOMG_13083 1,010,581-1,011,388 (+): mating-type protein MAT-1FOMG_13083FOMG_13084 1,012,210-1,016,675 (-): hypothetical proteinFOMG_13084FOMG_13085 1,017,836-1,019,995 (-): 50S ribosomal protein L21eFOMG_13085FOMG_13086 1,018,897-1,020,163 (+): 40S ribosomal protein S9FOMG_13086FOMG_13087 1,020,094-1,021,700 (-): pre-mRNA-splicing factor SLU7FOMG_13087
FungiDB release 68 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.
  • MAT1-1-5 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
JH659339.1:1,004,192–1,019,509 · 15.3 kb
Own genes
JH659339.1:1,004,192–1,019,509 · 15.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
277.7 kb
Region (samtools)
JH659339.1:1004192-1019509
Idiomorph scores
  • MAT1-2 402.0
  • MAT1-1 31.2

Margin over the next idiomorph: 370.8

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
MAT1-2-1100.0MAT1-1-340.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits1,004,192–1,004,953 -–578113_sxlc146_MAT_MAT1-2FOMG_13078
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%1.9e-226637 bits1,005,474–1,007,706 +–2903220_liq80xsp_MAT_combinedFOMG_13079
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%1.3e-1360 bits1,008,257–1,009,031 -–230073_uamh-1363_MAT_MAT1-1FOMG_13081
MAT1-2-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%2.5e-147402 bits1,008,257–1,009,031 -–61372_suf959_MAT_MAT1-2FOMG_13081
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,372 bits1,012,777–1,016,344 -–107463_unknown-1_MAT_MAT1-2FOMG_13084
MAT1-1-5core MATother idiomorph, not countedhit onlytblastn37.5cov 13.0%2.4e+0031 bits1,019,378–1,019,509 +–5180_44ba1_MAT_combinedFOMG_13085 (opposite strand)
FOMG_13086
MAT1-1-1expected, 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
MATJH659329.1:1,739,632–1,741,223MAT1-2MAT1-2-11too few of the family's genes found
MATJH659330.1:3,817,885–3,820,054MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
Foxysporum26406.genome.fasta
Assembly
1,146 contigs · 54.0 Mb · N50 2.2 Mb
Genome SHA-256
13d250366d00880dc79dad12fff4b6bd0c2ec720017e2afc92b1e3481bca380b
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
2026-11-07T01:58:48Z
Run time
90 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