MATPredict · mating-type report

BceratinophilaUAMH5669

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 01:55 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-1high confidenceMAT1-2medium confidence

Called loci 2

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on LJPH01004335.1MAT1-1 locus: genes from left to right on LJPH01004335.1, 979 to 7,743: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-4 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand).2 kb4 kb6 kb8 kbcontig endcalled locusCOX13: conserved flank, 979–1,656 (-), identity 89.78%, the two modelling tools disagreeCOX13APN2: conserved flank, 2,177–4,115 (+), identity 69.71%, the two modelling tools disagreeAPN2MAT1-1-4: core MAT gene, 4,946–5,543 (+), identity 68.42%, the two modelling tools disagreeMAT1-1-4MAT1-1-1: core MAT gene, 6,527–7,743 (+), identity 71.95%, gene modelMAT1-1-1
Gene order on LJPH01004335.1. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
Location
LJPH01004335.1:979–7,743 · 6.8 kb
Own genes
LJPH01004335.1:979–7,743 · 6.8 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 4 gene hits
Nearest contig end
804 bp
Region (samtools)
LJPH01004335.1:979-7743
Idiomorph scores
  • MAT1-1 407.0

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
COX13conserved flankmodels differexonerateminiprot: 976–1,656, 87.9%89.8cov 100.0%5.6e-30112 bits979–1,656 -5199306_rmscc1040_MAT_MAT1-1
APN2conserved flankmodels differexonerateminiprot: 2,032–4,115, 67.5%69.7cov 98.7%< 1e-180395 bits2,177–4,115 +4199306_rmscc1040_MAT_MAT1-1
MAT1-1-4core MATmodels differexonerateminiprot: 4,833–5,419, 69.1%68.4cov 69.9%1.5e-71237 bits4,946–5,543 +2199306_rmscc1040_MAT_MAT1-1
MAT1-1-1core MATgene modelexonerate72.0cov 99.7%2.3e-142407 bits6,527–7,743 +25501_h538-4_MAT_MAT1-1
SLA2expected, not found

MAT1-2 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-2 locus on LJPH01004302.1MAT1-2 locus: genes from left to right on LJPH01004302.1, 3 to 6,253: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, minus strand); CIMG_00407 (core MAT gene, plus strand); MAT1-2-4 (core MAT gene, plus strand).1 kb2 kb3 kb4 kb5 kb6 kbcontig endcalled locusCOX13: conserved flank, 3–382 (-), identity 80.23%, gene modelCOX13APN2: conserved flank, 664–2,061 (+), identity 80.69%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 3,687–4,888 (-), identity 72.31%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 4,178–4,651 (-), identity 26.875%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)CIMG_00407: core MAT gene, 5,356–6,250 (+), identity 67.05%, the two modelling tools disagreeCIMG_00407MAT1-2-4: core MAT gene, 5,975–6,226 (+), identity 28.571%, search hit onlyMAT1-2-4
Gene order on LJPH01004302.1. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
LJPH01004302.1:3–6,253 · 6.3 kb
Own genes
LJPH01004302.1:3–6,250 · 6.2 kb · the span runs 3 bp beyond these genes
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 6 gene hits
Nearest contig end
2 bp
Region (samtools)
LJPH01004302.1:3-6253
Idiomorph scores
  • MAT1-2 385.0

Margin over the set-aside MAT1-1-3 hit: 48.3 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
MAT1-2-175.2MAT1-1-326.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankgene modelexonerate80.2cov 65.2%4.8e-2187 bits3–382 -35501_rs_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 664–2,754, 62.9%80.7cov 63.7%< 1e-180650 bits664–2,061 +65501_rs_MAT_MAT1-2
MAT1-2-1core MATmodels differexonerateminiprot: 3,648–4,888, 67.1%72.3cov 97.3%5.5e-122385 bits3,687–4,888 -45501_rs_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn26.9cov 86.0%3.9e-0954 bits4,178–4,651 -–5127_mo44_MAT_MAT1-1
CIMG_00407core MATmodels differexonerateminiprot: 5,356–6,262, 66.0%67.0cov 99.6%1.6e-94245 bits5,356–6,250 +35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn28.6cov 27.0%3.6e-0740 bits5,975–6,226 +–746128_af293_MAT_MAT1-2
SLA2expected, not found

Withheld candidate loci 11

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 (11).

Show the 11 withheld loci

Withheld loci (11)

familylocationidiomorph genesmodelledreason
MATLJPH01001999.1:120,902–139,499MAT1-2MAT1-2-1, SLA21fewer than 2 genes could be modelled
MATLJPH01002249.1:14,224–21,689MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPH01001398.1:65,661–89,666MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPH01003720.1:26,789–36,158MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATLJPH01001052.1:303,316–337,179MAT1-2MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATLJPH01001282.1:20,484–21,168MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATLJPH01000314.1:96,606–114,956MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPH01000759.1:87,677–88,826MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPH01000858.1:294,103–306,547MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPH01000529.1:36,723–56,787MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATLJPH01002471.1:25,094–29,492MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled

Provenance

Genome file
BceratinophilaUAMH5669.genome.fasta
Assembly
4,851 contigs · 27.5 Mb · N50 103.5 kb
Genome SHA-256
a6c2ab5ce8d681e518f3baf7d9c9a67bf9c02c32f17debd22c66a28a00dcdb80
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': 33184, 'routing_taxid_rank': 'family', 'flags': ['high_N'], '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 33184', 'routed_by': 'family taxid 33184 (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
2026-11-07T01:54:40Z
Run time
67 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