MATPredict · mating-type report

NcrassaOR74A

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 02:02 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 CM002236MAT1-1 locus: genes from left to right on CM002236, 1,851,640 to 1,872,435: 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); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).1,855 kb1,860 kb1,865 kb1,870 kb← 1,850.6 kb more to contig endcalled locusCOX13: conserved flank, 1,851,640–1,852,342 (-), identity 73.4%, search hit onlyCOX13APN2: conserved flank, 1,853,299–1,855,571 (+), identity 79.5%, search hit onlyAPN2MAT1-1-3: core MAT gene, 1,857,194–1,858,331 (-), identity 100.0%, search hit onlyMAT1-1-3MAT1-2-1: core MAT gene, 1,857,500–1,857,637 (-), identity 32.609%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-2: core MAT gene, 1,859,093–1,860,424 (+), identity 97.3%, search hit onlyMAT1-1-2MAT1-1-1: core MAT gene, 1,860,834–1,861,834 (+), identity 100.0%, search hit onlyMAT1-1-1SLA2: conserved flank, 1,869,097–1,872,435 (-), identity 80.2%, search hit onlySLA2
Gene order on CM002236. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CM002236, 1,850,600 to 1,873,474NCU01963 1,848,061-1,851,346 (+): anaphase-promoting complex subunit Apc5NCU01963 eat-6NCU01962 1,851,072-1,852,772 (-): encodes anonymous transcript-5 protein, variant 1NCU01962 eat-5NCU01961 1,853,043-1,855,879 (+): DNA lyase Apn2, variant 1NCU01961 apn-2NCU01960 1,857,194-1,858,469 (-): mating-type protein A-3NCU01960 matA-3NCU01959 1,859,093-1,860,424 (+): mating-type protein A-2NCU01959 matA-2NCU01958 1,860,692-1,862,194 (+): mating-type protein A-1, variant 1NCU01958 matA-1NCU14009 1,862,928-1,864,066 (+): unspecified productNCU14009NCU01957 1,865,597-1,867,210 (-): AR2NCU01957 eat-2ANCU01956 1,868,552-1,872,864 (-): cytoskeleton assembly control protein Sla2NCU01956 eat-2NCU01955 1,873,289-1,875,362 (+): autophagocytosis protein Aut1NCU01955 apg-3
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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CM002236:1,851,640–1,872,435 · 20.8 kb
Own genes
CM002236:1,851,640–1,872,435 · 20.8 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
1.9 Mb
Region (samtools)
CM002236:1851640-1872435
Idiomorph scores
  • MAT1-1 723.0

Margin over the set-aside MAT1-2-1 hit: 67.4 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
MAT1-1-3100.0MAT1-2-132.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome73.4cov 58.5%2.4e-51152 bits1,851,640–1,852,342 -–5501_rs_MAT_MAT1-2NCU01962 eat-5
APN2conserved flankhit onlyDIAMOND, proteome79.5cov 36.7%7.4e-240672 bits1,853,299–1,855,571 +–2903220_liq80xsp_MAT_combinedNCU01961 apn-2
MAT1-1-3core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.3e-238642 bits1,857,194–1,858,331 -–5141_74-ors-a_MAT_MAT1-1NCU01960 matA-3
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn32.6cov 36.0%1.9e-0131 bits1,857,500–1,857,637 -–61372_suf959_MAT_MAT1-2NCU01960 matA-3
MAT1-1-2core MAThit onlyDIAMOND, proteome97.3cov 98.7%3.4e-269723 bits1,859,093–1,860,424 +–5141_74-ors-a_MAT_MAT1-1NCU01959 matA-2
MAT1-1-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%4.4e-226607 bits1,860,834–1,861,834 +–5141_74-ors-a_MAT_MAT1-1NCU01958 matA-1
SLA2conserved flankhit onlyDIAMOND, proteome80.2cov 100.0%< 1e-1801,328 bits1,869,097–1,872,435 -–230073_uamh-1363_MAT_MAT1-1NCU01956 eat-2

Withheld candidate loci 3

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 (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATCM002236:3,502,631–3,504,624MAT1-2MAT1-2-11too few of the family's genes found
MATCM002237:526,083–546,123MAT1-2MAT1-2-1, MAT1-1-21too few of the family's genes found
MATCM002242:2,905,412–2,907,637MAT1-2MAT1-2-1, MAT1-1-21too few of the family's genes found

Provenance

Genome file
NcrassaOR74A.genome.fasta
Assembly
21 contigs · 41.1 Mb · N50 6.0 Mb
Genome SHA-256
d581eec06534b1d0ab4218ae208e74abbfaf622c4720eaa376a687ed46c7dd8a
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': 5148, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 5148', 'routed_by': 'family taxid 5148 (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
2026-11-07T02:01:03Z
Run time
100 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