MATPredict · mating-type report

Foxysporumrace1

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 02:08 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 KB730167MAT1-2 locus: genes from left to right on KB730167, 361,773 to 378,329: 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).365 kb370 kb375 kb274.0 kb more to contig end →called locusCOX13: conserved flank, 361,773–362,534 (-), identity 69.8%, search hit onlyCOX13APN2: conserved flank, 363,055–365,287 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 365,838–366,612 (-), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 365,838–366,612 (-), identity 100.0%, search hit onlyMAT1-2-1SLA2: conserved flank, 371,599–372,099 (-), identity 88.4%, search hit onlySLA2MAT1-1-5: core MAT gene, 378,198–378,329 (+), identity 37.5%, search hit onlyMAT1-1-5
Gene order on KB730167. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on KB730167, 360,945 to 379,156FOC1_g10008447 361,773-362,534 (-): Cytochrome c oxidase subunit 6A, mitochondrialFOC1_g10008447FOC1_g10008448 363,055-365,287 (+): DNA-(apurinic or apyrimidinic site) lyase 2FOC1_g10008448FOC1_g10008449 365,838-366,612 (-): Mating-type protein a-1FOC1_g10008449FOC1_g10008450 368,162-368,969 (+): hypothetical proteinFOC1_g10008450FOC1_g10008451 369,929-370,187 (-): hypothetical proteinFOC1_g10008451FOC1_g10008452 371,599-372,099 (-): Endocytosis protein end4FOC1_g10008452FOC1_g10008453 372,783-375,166 (-): Endocytosis protein end4FOC1_g10008453FOC1_g10008454 376,920-377,594 (-): 60S ribosomal protein L21-AFOC1_g10008454FOC1_g10008455 377,973-378,691 (+): 40S ribosomal protein S9FOC1_g10008455FOC1_g10008456 379,014-380,417 (-): Pre-mRNA-splicing factor SLU7FOC1_g10008456
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
KB730167:361,773–378,329 · 16.6 kb
Own genes
KB730167:361,773–378,329 · 16.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
274.8 kb
Region (samtools)
KB730167:361773-378329
Idiomorph scores
  • MAT1-2 403.0
  • MAT1-1 31.6

Margin over the next idiomorph: 371.4

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome69.8cov 89.2%9.2e-63181 bits361,773–362,534 -–578113_sxlc146_MAT_MAT1-2FOC1_g10008447
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%9.2e-219617 bits363,055–365,287 +–2903220_liq80xsp_MAT_combinedFOC1_g10008448
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%1.3e-1360 bits365,838–366,612 -–230073_uamh-1363_MAT_MAT1-1FOC1_g10008449
MAT1-2-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.8e-147403 bits365,838–366,612 -–61372_suf959_MAT_MAT1-2FOC1_g10008449
SLA2conserved flankhit onlyDIAMOND, proteome88.4cov 8.2%1.8e-270767 bits371,599–372,099 -–578113_sxlc146_MAT_MAT1-2FOC1_g10008452
MAT1-1-5core MATother idiomorph, not countedhit onlytblastn37.5cov 13.0%1.4e+0032 bits378,198–378,329 +–5180_44ba1_MAT_combinedFOC1_g10008455
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
MATKB730134:48,925–50,516MAT1-2MAT1-2-11too few of the family's genes found
MATKB730248:860,778–862,956MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
Foxysporumrace1.genome.fasta
Assembly
1,341 contigs · 47.7 Mb · N50 653.1 kb
Genome SHA-256
120e530a40bdafe93ddd043af3f78acda5e74cdce7cb8781c7b7171e6c1c4b74
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
2026-11-07T02:06:50Z
Run time
81 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