MATPredict · mating-type report

FoxysporumFo47

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

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on JH717900.1MAT1-2 locus: genes from left to right on JH717900.1, 789,716 to 805,026: MAT1-1-5 (core MAT gene, minus strand); SLA2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).790 kb795 kb800 kb805 kb← 789.0 kb more to contig endcalled locusMAT1-1-5: core MAT gene, 789,716–789,847 (-), identity 37.5%, search hit onlyMAT1-1-5SLA2: conserved flank, 792,873–796,441 (+), identity 81.6%, search hit onlySLA2MAT1-1-3: core MAT gene, 800,187–800,961 (+), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 800,187–800,961 (+), identity 99.2%, search hit onlyMAT1-2-1APN2: conserved flank, 801,512–803,744 (-), identity 86.4%, search hit onlyAPN2COX13: conserved flank, 804,265–805,026 (+), identity 69.8%, search hit onlyCOX13
Gene order on JH717900.1. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on JH717900.1, 788,951 to 805,792FOZG_08369 787,525-789,131 (+): pre-mRNA-splicing factor SLU7FOZG_08369FOZG_08370 789,063-790,328 (-): 40S ribosomal protein S9FOZG_08370FOZG_08371 789,230-791,389 (+): 50S ribosomal protein L21eFOZG_08371FOZG_08372 792,542-797,008 (+): I/LWEQ domain | ANTH domain | domain-containing proteinFOZG_08372FOZG_08373 797,830-798,637 (-): mating-type protein MAT-1FOZG_08373FOZG_08374 799,721-799,834 (-): hypothetical proteinFOZG_08374FOZG_08375 800,187-800,961 (+): HMG (high mobility group) box | domain-containing proteinFOZG_08375FOZG_08376 800,991-801,289 (+): hypothetical proteinFOZG_08376FOZG_08377 801,323-804,054 (-): AP endonuclease 2FOZG_08377FOZG_08378 804,172-805,342 (+): cytochrome c oxidase subunit 6aFOZG_08378FOZG_08379 805,437-809,600 (+): anaphase-promoting complex subunit 5FOZG_08379
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.
  • MAT1-1-5 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
JH717900.1:789,716–805,026 · 15.3 kb
Own genes
JH717900.1:789,716–805,026 · 15.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
789.7 kb
Region (samtools)
JH717900.1:789716-805026
Idiomorph scores
  • MAT1-2 402.0
  • MAT1-1 31.6

Margin over the next idiomorph: 370.4

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
MAT1-2-199.2MAT1-1-340.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-5core MATother idiomorph, not countedhit onlytblastn37.5cov 13.0%1.5e+0032 bits789,716–789,847 -–5180_44ba1_MAT_combinedFOZG_08370
FOZG_08371 (opposite strand)
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,372 bits792,873–796,441 +–107463_unknown-1_MAT_MAT1-2FOZG_08372
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%1.3e-1360 bits800,187–800,961 +–230073_uamh-1363_MAT_MAT1-1FOZG_08375
MAT1-2-1core MAThit onlyDIAMOND, proteome99.2cov 100.0%3.6e-147402 bits800,187–800,961 +–61372_suf959_MAT_MAT1-2FOZG_08375
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%6.1e-225633 bits801,512–803,744 -–2903220_liq80xsp_MAT_combinedFOZG_08377
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits804,265–805,026 +–578113_sxlc146_MAT_MAT1-2FOZG_08378
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
MATJH717896.1:1,737,693–1,739,284MAT1-2MAT1-2-11too few of the family's genes found
MATJH717897.1:3,809,849–3,812,018MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FoxysporumFo47.genome.fasta
Assembly
124 contigs · 49.7 Mb · N50 3.8 Mb
Genome SHA-256
f64f6d63a4e90ef3979772f4713d02e0654418d8b822cbd53ed7f4509442d6f5
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
2026-11-07T02:34:12Z
Run time
98 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