MATPredict · mating-type report

VdahliaeJR2

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 02:09 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 CP009079.1MAT1-2 locus: genes from left to right on CP009079.1, 3,830,361 to 3,865,912: MAT1-1-3 (core MAT gene, plus strand); SLA2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).3,830 kb3,840 kb3,850 kb3,860 kb410.1 kb more to contig end →called locusMAT1-1-3: core MAT gene, 3,830,361–3,830,450 (+), identity 30.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)SLA2: conserved flank, 3,848,203–3,851,663 (+), identity 98.2%, search hit onlySLA2MAT1-2-1: core MAT gene, 3,859,641–3,860,439 (+), identity 99.6%, search hit onlyMAT1-2-1APN2: conserved flank, 3,862,166–3,864,535 (-), identity 100.0%, search hit onlyAPN2COX13: conserved flank, 3,865,000–3,865,912 (+), identity 90.2%, search hit onlyCOX13
Gene order on CP009079.1. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP009079.1, 3,828,586 to 3,867,686VDAG_JR2_Chr2g11780a 3,826,305-3,833,782 (+): unspecified productVDAG_JR2_Chr2g11780aVDAG_JR2_Chr2g11790a 3,834,143-3,837,586 (+): unspecified productVDAG_JR2_Chr2g11790aVDAG_JR2_Chr2g11800a 3,837,796-3,843,191 (-): unspecified productVDAG_JR2_Chr2g11800aVDAG_JR2_Chr2g11810a 3,843,359-3,845,025 (+): unspecified productVDAG_JR2_Chr2g11810aVDAG_JR2_Chr2g11820a 3,845,063-3,845,986 (-): unspecified productVDAG_JR2_Chr2g11820aVDAG_JR2_Chr2g11830a 3,846,082-3,847,295 (+): unspecified productVDAG_JR2_Chr2g11830aVDAG_JR2_Chr2g11840a 3,847,927-3,851,957 (+): unspecified productVDAG_JR2_Chr2g11840aVDAG_JR2_Chr2g11850a 3,856,996-3,858,417 (-): unspecified productVDAG_JR2_Chr2g11850aVDAG_JR2_Chr2g11860a 3,859,536-3,860,574 (+): unspecified productVDAG_JR2_Chr2g11860aVDAG_JR2_Chr2g11870a 3,861,994-3,864,600 (-): unspecified productVDAG_JR2_Chr2g11870aVDAG_JR2_Chr2g11880a 3,864,970-3,865,945 (+): unspecified productVDAG_JR2_Chr2g11880aVDAG_JR2_Chr2g11890a 3,866,015-3,868,983 (-): unspecified productVDAG_JR2_Chr2g11890a
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.
Location
CP009079.1:3,830,361–3,865,912 · 35.6 kb
Own genes
CP009079.1:3,830,361–3,865,912 · 35.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
411.9 kb
Region (samtools)
CP009079.1:3830361-3865912
Idiomorph scores
  • MAT1-2 449.0
  • MAT1-1 31.6

Margin over the next idiomorph: 417.4

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
MAT1-2-199.6MAT1-1-325.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn30.0cov 19.0%2.8e-0132 bits3,830,361–3,830,450 +–5127_mo44_MAT_MAT1-1VDAG_JR2_Chr2g11780a
SLA2conserved flankhit onlyDIAMOND, proteome98.2cov 100.0%< 1e-1801,693 bits3,848,203–3,851,663 +–27337_vdls-17_MAT_MAT1-2VDAG_JR2_Chr2g11840a
MAT1-2-1core MAThit onlyDIAMOND, proteome99.6cov 100.0%1.3e-165449 bits3,859,641–3,860,439 +–27337_vdls-17_MAT_MAT1-2VDAG_JR2_Chr2g11860a
APN2conserved flankhit onlyDIAMOND, proteome100.0cov 96.9%< 1e-1801,061 bits3,862,166–3,864,535 -–27337_vdls-17_MAT_MAT1-2VDAG_JR2_Chr2g11870a
COX13conserved flankhit onlyDIAMOND, proteome90.2cov 100.0%6.6e-85238 bits3,865,000–3,865,912 +–27337_vdls-17_MAT_MAT1-2VDAG_JR2_Chr2g11880a
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
MATCP009077.1:2,326,444–2,328,130MAT1-2MAT1-2-11too few of the family's genes found
MATCP009080.1:1,946,011–1,948,429MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
VdahliaeJR2.genome.fasta
Assembly
8 contigs · 36.2 Mb · N50 4.2 Mb
Genome SHA-256
d14b18d4c82915e7843c28982d4985b3969e8a6f659f79d8350a95ac362dcbfc
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': 1033978, '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 1033978', 'routed_by': 'family taxid 1033978 (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
2026-11-07T02:07:36Z
Run time
88 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