MATPredict · mating-type report

BgilchristiiSLH14081

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 02:03 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2medium confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on GG657461MAT1-2 locus: genes from left to right on GG657461, 1,036,425 to 1,047,219: CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-4 (core MAT gene, minus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand).1,036 kb1,038 kb1,040 kb1,042 kb1,044 kb1,046 kb627.7 kb more to contig end →called locusCIMG_00407: core MAT gene, 1,036,425–1,037,032 (-), identity 40.62%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 1,036,541–1,037,023 (-), identity 25.466%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 1,037,871–1,039,012 (+), identity 39.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,037,871–1,039,012 (+), identity 52.4%, search hit onlyMAT1-2-1MAT1-1-4: core MAT gene, 1,040,186–1,040,887 (-), identity 40.2%, search hit onlyMAT1-1-4COX13: conserved flank, 1,043,680–1,044,604 (-), identity 80.4%, search hit onlyCOX13APN2: conserved flank, 1,044,952–1,047,219 (+), identity 71.1%, search hit onlyAPN2
Gene order on GG657461. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on GG657461, 1,035,886 to 1,047,759BDBG_06645 1,035,424-1,037,531 (-): unspecified productBDBG_06645BDBG_06646 1,035,426-1,039,721 (+): HMG domain-containing protein, variant 4BDBG_06646BDBG_06647 1,039,410-1,041,026 (-): hypothetical protein, variantBDBG_06647BDBG_06648 1,041,730-1,043,297 (-): unspecified productBDBG_06648BDBG_06649 1,043,377-1,048,515 (-): cytochrome c oxidase subunit 6aBDBG_06649BDBG_06650 1,044,806-1,048,538 (+): AP endonuclease 2BDBG_06650
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
  • gene model
  • search hit only
Location
GG657461:1,036,425–1,047,219 · 10.8 kb
Own genes
GG657461:1,036,425–1,047,219 · 10.8 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 7 gene hits
Nearest contig end
628.3 kb
Region (samtools)
GG657461:1036425-1047219
Idiomorph scores
  • MAT1-2 304.0
  • MAT1-1 83.6

Margin over the next idiomorph: 220.4

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
MAT1-2-152.4MAT1-1-339.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
CIMG_00407core MATgene modelexonerate40.6cov 62.4%2.9e-32125 bits1,036,425–1,037,032 -35501_rs_MAT_MAT1-2BDBG_06645
BDBG_06646 (opposite strand)
MAT1-2-4core MAThit onlytblastn25.5cov 57.0%9.7e-1266 bits1,036,541–1,037,023 -–746128_af293_MAT_MAT1-2BDBG_06645
BDBG_06646 (opposite strand)
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome39.0cov 45.6%2.6e-1257 bits1,037,871–1,039,012 +–230073_uamh-1363_MAT_MAT1-1BDBG_06646
MAT1-2-1core MAThit onlyDIAMOND, proteome52.4cov 21.8%1.1e-104304 bits1,037,871–1,039,012 +–40559_sas405_MAT_MAT1-2BDBG_06646
MAT1-1-4core MAThit onlyDIAMOND, proteome40.2cov 48.8%1.6e-2284 bits1,040,186–1,040,887 -–199306_rmscc1040_MAT_MAT1-1BDBG_06647
COX13conserved flankhit onlyDIAMOND, proteome80.4cov 83.0%3.2e-59173 bits1,043,680–1,044,604 -–5501_rs_MAT_MAT1-2BDBG_06649
APN2conserved flankhit onlyDIAMOND, proteome71.1cov 86.5%4.6e-255710 bits1,044,952–1,047,219 +–27339_unknown-1_MAT_MAT1-2BDBG_06649 (opposite strand)
BDBG_06650
MAT1-1-1expected, not found–
SLA2expected, 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
MATGG657452:2,811,014–2,813,325MAT1-2MAT1-2-11too few of the family's genes found
MATGG657461:992,045–996,345undeterminedSLA21too few of the family's genes found

Provenance

Genome file
BgilchristiiSLH14081.genome.fasta
Assembly
103 contigs · 75.4 Mb · N50 2.4 Mb
Genome SHA-256
b082df519e0eec368eed72f1ed877d1e1fd3d527ec20489aff6be706ed4a07d2
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': 299071, '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 299071', 'routed_by': 'family taxid 299071 (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
2026-11-07T02:01:36Z
Run time
126 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