MATPredict · mating-type report

AnigerLDM3

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

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on VTFN01000007MAT1-1 locus: genes from left to right on VTFN01000007, 1,613,634 to 1,645,106: SLA2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, plus strand).1,615 kb1,620 kb1,625 kb1,630 kb1,635 kb1,640 kb1,645 kb← 1,612.1 kb more to contig endcalled locusSLA2: conserved flank, 1,613,637–1,617,372 (+), identity 92.65%, gene modelSLA2MAT1-1-3: core MAT gene, 1,630,442–1,630,534 (+), identity 41.935%, search hit onlyMAT1-1-3COX13: conserved flank, 1,638,299–1,638,974 (-), identity 84.8%, the two modelling tools disagreeCOX13APN2: conserved flank, 1,639,546–1,641,675 (+), identity 73.43%, gene modelAPN2MAT1-1-1: core MAT gene, 1,643,955–1,644,833 (+), identity 60.36%, the two modelling tools disagreeMAT1-1-1
Gene order on VTFN01000007. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
Location
VTFN01000007:1,613,634–1,645,106 · 31.5 kb
Own genes
VTFN01000007:1,613,637–1,644,833 · 31.2 kb · the span runs 276 bp beyond these genes
Supported span
VTFN01000007:1,613,637–1,645,106 · 31.5 kb · 3 bp of the reported span rests only on hits below 33 bits
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.6 Mb
Region (samtools)
VTFN01000007:1613634-1645106
Idiomorph scores
  • MAT1-1 343.0

No other idiomorph scored.

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankgene modelexonerate92.7cov 88.8%< 1e-180743 bits1,613,637–1,617,372 +11746128_a1163_MAT_MAT1-1
MAT1-1-3core MAThit onlytblastn41.9cov 17.0%7.7e+0027 bits1,630,442–1,630,534 +–5518_3639_MAT_combined
COX13conserved flankmodels differexonerateminiprot: 1,638,296–1,639,010, 82.5%2 frameshiftsdefective gene model84.8cov 94.1%5.1e-41144 bits1,638,299–1,638,974 -5746128_af293_MAT_MAT1-2
APN2conserved flankgene modelexonerate1 frameshiftdefective gene model73.4cov 98.9%< 1e-180523 bits1,639,546–1,641,675 +5746128_a1163_MAT_MAT1-1
MAT1-1-1core MATmodels differexonerateminiprot: 1,643,955–1,645,112, 49.5%60.4cov 75.0%2.1e-106343 bits1,643,955–1,644,833 +2746128_a1163_MAT_MAT1-1

Withheld candidate loci 24

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: fewer than 2 genes could be modelled (24).

Show the 24 withheld loci

Withheld loci (24)

familylocationidiomorph genesmodelledreason
MATVTFN01000007:1,228,349–1,241,525MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000007:1,455,330–1,465,567MAT1-1MAT1-1-1, SLA2, MAT1-1-30fewer than 2 genes could be modelled
MATVTFN01000005:5,895,809–5,914,724MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATVTFN01000001:1,773,131–1,797,946MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATVTFN01000001:2,298,014–2,332,270MAT1-1SLA2, COX13, MAT1-1-30fewer than 2 genes could be modelled
MATVTFN01000001:2,950,556–2,994,604MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATVTFN01000001:4,387,449–4,394,302MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000002:1,388,583–1,393,900MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATVTFN01000002:2,186,417–2,214,425MAT1-1MAT1-1-1, SLA2, COX130fewer than 2 genes could be modelled
MATVTFN01000002:2,608,921–2,628,931MAT1-2MAT1-2-1, APN2, COX130fewer than 2 genes could be modelled
MATVTFN01000004:89,514–91,846MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000012:535,275–557,451MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATVTFN01000006:502,487–525,241MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATVTFN01000006:963,772–984,026MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATVTFN01000006:3,685,661–3,711,111undeterminedMAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000006:3,855,672–3,889,003MAT1-1MAT1-1-1, APN2, COX130fewer than 2 genes could be modelled
MATVTFN01000003:1,105,834–1,122,750MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATVTFN01000003:2,701,531–2,716,004MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATVTFN01000003:3,881,908–3,897,096MAT1-1MAT1-1-1, MAT1-2-1, COX130fewer than 2 genes could be modelled
MATVTFN01000009:2,175,066–2,200,424MAT1-2APN2, COX13, MAT1-2-40fewer than 2 genes could be modelled
MATVTFN01000009:2,271,795–2,291,943MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000009:2,508,363–2,513,542MAT1-1MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATVTFN01000009:2,693,116–2,716,037MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATVTFN01000010:520,133–543,541MAT1-2MAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled

Provenance

Genome file
AnigerLDM3.genome.fasta
Assembly
14 contigs · 35.3 Mb · N50 4.0 Mb
Genome SHA-256
d06823543bc7eae7dfbfdb5eb855cdc5a27f3de0978464804aaaa03875797e69
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': 1131492, '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 1131492', 'routed_by': 'family taxid 1131492 (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
2026-11-07T02:02:21Z
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