MATPredict · mating-type report

FnapiformeNRRL25196

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 JAAOAO010000075MAT1-2 locus: genes from left to right on JAAOAO010000075, 15,125 to 28,498: 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).15 kb20 kb25 kb← 14.5 kb more to contig endcalled locusSLA2: conserved flank, 15,125–18,711 (+), identity 81.6%, search hit onlySLA2MAT1-1-3: core MAT gene, 23,662–24,436 (+), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 23,662–24,436 (+), identity 91.0%, search hit onlyMAT1-2-1APN2: conserved flank, 25,204–27,219 (-), identity 86.4%, search hit onlyAPN2COX13: conserved flank, 27,736–28,498 (+), identity 70.7%, search hit onlyCOX13
Gene order on JAAOAO010000075. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on JAAOAO010000075, 14,457 to 29,165FNAPI_2097 15,125-18,711 (+): cytoskeleton assembly control SLA2FNAPI_2097FNAPI_2098 21,307-22,117 (-): mating type MAT1-2-3FNAPI_2098FNAPI_2099 23,662-24,436 (+): mating typeFNAPI_2099FNAPI_2100 25,204-27,219 (-): AP endonuclease 2FNAPI_2100FNAPI_2101 27,736-28,498 (+): cytochrome c oxidase subunit 6aFNAPI_2101
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
JAAOAO010000075:15,125–28,498 · 13.4 kb
Own genes
JAAOAO010000075:15,125–28,498 · 13.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
15.1 kb
Region (samtools)
JAAOAO010000075:15125-28498
Idiomorph scores
  • MAT1-2 405.0

Margin over the set-aside MAT1-1-3 hit: 50.7 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
MAT1-2-191.0MAT1-1-340.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,372 bits15,125–18,711 +–107463_unknown-1_MAT_MAT1-2FNAPI_2097
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%9.4e-1460 bits23,662–24,436 +–230073_uamh-1363_MAT_MAT1-1FNAPI_2099
MAT1-2-1core MAThit onlyDIAMOND, proteome91.0cov 100.0%2.2e-148405 bits23,662–24,436 +–5127_mo45_MAT_MAT1-2FNAPI_2099
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%3.2e-220616 bits25,204–27,219 -–2903220_liq80xsp_MAT_combinedFNAPI_2100
COX13conserved flankhit onlyDIAMOND, proteome70.7cov 89.2%1.6e-63183 bits27,736–28,498 +–578113_sxlc146_MAT_MAT1-2FNAPI_2101

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
MATJAAOAO010000265:78,552–80,721MAT1-2MAT1-2-11too few of the family's genes found
MATJAAOAO010000377:20,562–26,685MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FnapiformeNRRL25196.genome.fasta
Assembly
1,411 contigs · 42.1 Mb · N50 78.4 kb
Genome SHA-256
fc1526a49a0e753720499f4debbe08fbc966cc6534e929185fd0b19e7fbca5e4
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': 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
2026-11-07T02:25:56Z
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