MATPredict · mating-type report

AmutatusUAMH3576

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 01:56 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 LJPJ01000748.1MAT1-1 locus: genes from left to right on LJPJ01000748.1, 515,780 to 526,740: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand); APN2 (conserved flank, minus strand).516 kb518 kb520 kb522 kb524 kb526 kbcontig endcalled locusSLA2: conserved flank, 515,780–519,719 (+), identity 97.04%, gene modelSLA2MAT1-1-1: core MAT gene, 521,173–522,385 (-), identity 63.45%, gene modelMAT1-1-1MAT1-1-4: core MAT gene, 523,294–523,898 (-), identity 64.16%, the two modelling tools disagreeMAT1-1-4APN2: conserved flank, 524,673–526,740 (-), identity 69.83%, the two modelling tools disagreeAPN2
Gene order on LJPJ01000748.1. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
Location
LJPJ01000748.1:515,780–526,740 · 11.0 kb
Own genes
LJPJ01000748.1:515,780–526,740 · 11.0 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 4 gene hits
Nearest contig end
339 bp
Region (samtools)
LJPJ01000748.1:515780-526740
Idiomorph scores
  • MAT1-1 362.0

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 modelexonerate97.0cov 100.0%< 1e-180800 bits515,780–519,719 +125501_rs_MAT_MAT1-2
MAT1-1-1core MATgene modelexonerate63.5cov 99.2%3.8e-128362 bits521,173–522,385 -2199306_rmscc1040_MAT_MAT1-1
MAT1-1-4core MATmodels differexonerateminiprot: 523,178–524,012, 56.0%64.2cov 70.7%1.9e-71236 bits523,294–523,898 -2199306_rmscc1040_MAT_MAT1-1
APN2conserved flankmodels differexonerateminiprot: 524,670–526,740, 68.7%69.8cov 100.0%< 1e-180405 bits524,673–526,740 -6199306_rmscc1040_MAT_MAT1-1
COX13expected, not found

Withheld candidate loci 16

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 (16).

Show the 16 withheld loci

Withheld loci (16)

familylocationidiomorph genesmodelledreason
MATLJPJ01000748.1:29,885–50,782MAT1-2MAT1-2-1, APN2, SLA20fewer than 2 genes could be modelled
MATLJPJ01000311.1:263,256–265,054MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATLJPJ01000463.1:21,493–29,739MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATLJPJ01000230.1:161,064–169,577MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPJ01000505.1:307,070–326,471MAT1-1MAT1-1-1, APN2, COX130fewer than 2 genes could be modelled
MATLJPJ01000408.1:9,902–13,768MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATLJPJ01000408.1:40,083–63,360MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPJ01000285.1:40,051–67,412MAT1-1MAT1-1-1, COX13, MAT1-1-30fewer than 2 genes could be modelled
MATLJPJ01000884.1:45,171–69,434MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPJ01000459.1:66,294–85,823MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPJ01000583.1:282,529–287,560MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPJ01000711.1:87,677–125,770MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATLJPJ01000035.1:145,792–161,092MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPJ01002452.1:34,845–47,691MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPJ01002068.1:301,317–309,073MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPJ01000361.1:109,056–120,008MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled

Provenance

Genome file
AmutatusUAMH3576.genome.fasta
Assembly
3,075 contigs · 30.4 Mb · N50 217.8 kb
Genome SHA-256
a804f966d8554665ff235cb7ef5dabef4ef4075838d2c4ac496a0cb3845e6d40
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': 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
2026-11-07T01:55:46Z
Run time
70 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