MATPredict · mating-type report

AmnigerUAMH3544

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 01:53 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 LJPK01002855.1MAT1-2 locus: genes from left to right on LJPK01002855.1, 79,638 to 90,873: SLA2 (conserved flank, plus strand); CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).80 kb82 kb84 kb86 kb88 kb90 kb← 79.1 kb more to contig endcalled locusSLA2: conserved flank, 79,638–83,555 (+), identity 95.9%, gene modelSLA2CIMG_00407: core MAT gene, 84,727–85,594 (-), identity 56.75%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 84,843–84,944 (-), identity 41.176%, search hit onlyMAT1-2-4MAT1-2-1: core MAT gene, 86,036–87,160 (+), identity 68.28%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 86,432–86,728 (+), identity 31.313%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)APN2: conserved flank, 87,832–89,896 (-), identity 67.45%, the two modelling tools disagreeAPN2COX13: conserved flank, 90,215–90,873 (+), identity 86.47%, the two modelling tools disagreeCOX13
Gene order on LJPK01002855.1. 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
LJPK01002855.1:79,638–90,873 · 11.2 kb
Own genes
LJPK01002855.1:79,638–90,873 · 11.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
79.6 kb
Region (samtools)
LJPK01002855.1:79638-90873
Idiomorph scores
  • MAT1-2 412.0

Margin over the set-aside MAT1-1-3 hit: 32.3 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
MAT1-2-163.6MAT1-1-331.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankgene modelexonerate95.9cov 100.0%< 1e-1801,496 bits79,638–83,555 +125501_rs_MAT_MAT1-2
CIMG_00407core MATgene modelexonerate56.8cov 96.6%3.1e-71204 bits84,727–85,594 -35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn41.2cov 14.0%9.0e-0331 bits84,843–84,944 -–746128_af293_MAT_MAT1-2
MAT1-2-1core MATmodels differexonerateminiprot: 86,036–87,169, 63.1%68.3cov 100.0%8.5e-131412 bits86,036–87,160 +3199306_silveira_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn31.3cov 45.0%1.2e-0957 bits86,432–86,728 +–230073_uamh-1363_MAT_MAT1-1
APN2conserved flankmodels differexonerateminiprot: 87,829–89,896, 66.8%67.5cov 100.0%< 1e-180409 bits87,832–89,896 -65501_rs_MAT_MAT1-2
COX13conserved flankmodels differexonerateminiprot: 90,215–90,876, 88.9%86.5cov 100.0%1.7e-31117 bits90,215–90,873 +45501_rs_MAT_MAT1-2

Withheld candidate loci 10

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 (9); too few of the family's genes found (1).

Show the 10 withheld loci

Withheld loci (10)

familylocationidiomorph genesmodelledreason
MATLJPK01000061.1:203,697–215,297MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPK01002079.1:5,905–7,374MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPK01001929.1:14,796–18,619MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPK01000953.1:106,471–158,165MAT1-2MAT1-1-1, APN2, COX13, MAT1-2-100fewer than 2 genes could be modelled
MATLJPK01000608.1:98,122–112,769MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPK01003212.1:46,347–61,341MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPK01000421.1:26,188–38,656MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPK01002853.1:20,609–41,080MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPK01000197.1:224,171–231,670MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPK01000541.1:394,256–397,422MAT1-2MAT1-2-1, MAT1-1-41too few of the family's genes found

Provenance

Genome file
AmnigerUAMH3544.genome.fasta
Assembly
3,481 contigs · 36.7 Mb · N50 98.9 kb
Genome SHA-256
878170883297496bb8d3a737dbe7493447b92c45f230750e82a364ac8ad3b42d
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
2026-11-07T01:51:50Z
Run time
76 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