MATPredict · mating-type report

CimmitisRMSCC2394

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 01:49 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 DS028093.1MAT1-2 locus: genes from left to right on DS028093.1, 1,149,675 to 1,163,183: 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); SLA2 (conserved flank, minus strand).1,150 kb1,155 kb1,160 kb← 1,149.0 kb more to contig endcalled locusCOX13: conserved flank, 1,149,675–1,150,340 (-), identity 100.0%, gene modelCOX13APN2: conserved flank, 1,150,960–1,153,013 (+), identity 100.0%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 1,153,751–1,154,877 (-), identity 100.0%, gene modelMAT1-2-1MAT1-1-3: core MAT gene, 1,154,147–1,154,638 (-), identity 26.829%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)CIMG_00407: core MAT gene, 1,155,322–1,156,215 (+), identity 100.0%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 1,155,960–1,156,082 (+), identity 34.146%, search hit onlyMAT1-2-4SLA2: conserved flank, 1,159,253–1,163,183 (-), identity 100.0%, gene modelSLA2
Gene order on DS028093.1. 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
DS028093.1:1,149,675–1,163,183 · 13.5 kb
Own genes
DS028093.1:1,149,675–1,163,183 · 13.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
1.1 Mb
Region (samtools)
DS028093.1:1149675-1163183
Idiomorph scores
  • MAT1-2 570.0

Margin over the set-aside MAT1-1-3 hit: 66.8 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
MAT1-2-193.6MAT1-1-326.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankgene modelexonerate100.0cov 100.0%4.1e-34124 bits1,149,675–1,150,340 -55501_rs_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 1,150,960–1,153,016, 96.6%100.0cov 100.0%< 1e-1801,095 bits1,150,960–1,153,013 +65501_rs_MAT_MAT1-2
MAT1-2-1core MATgene modelexonerate100.0cov 100.0%< 1e-180570 bits1,153,751–1,154,877 -35501_rs_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn26.8cov 86.0%2.2e-0852 bits1,154,147–1,154,638 -–5127_mo44_MAT_MAT1-1
CIMG_00407core MATgene modelexonerate100.0cov 100.0%7.9e-146369 bits1,155,322–1,156,215 +35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn34.1cov 16.0%9.1e-0736 bits1,155,960–1,156,082 +–746128_af293_MAT_MAT1-2
SLA2conserved flankgene modelexonerate100.0cov 100.0%< 1e-180911 bits1,159,253–1,163,183 -125501_rs_MAT_MAT1-2

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
MATDS028093.1:1,364,506–1,388,766MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS028093.1:3,460,504–3,462,415MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS028093.1:4,254,870–4,278,115MAT1-1APN2, COX13, MAT1-1-20fewer than 2 genes could be modelled
MATDS028093.1:4,938,184–4,945,431MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS028094.1:3,522,875–3,543,953MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS028094.1:3,897,355–3,932,417MAT1-2MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS028097.1:200,227–201,871MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS028097.1:2,312,267–2,327,957MAT1-1MAT1-1-1, APN2, MAT1-1-50fewer than 2 genes could be modelled
MATDS028096.1:669,409–688,446MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS028096.1:1,407,904–1,431,606MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS028096.1:2,197,673–2,205,315MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS028096.1:3,196,860–3,249,756MAT1-1MAT1-1-1, MAT1-2-1, APN2, MAT1-1-30fewer than 2 genes could be modelled
MATDS028099.1:468,892–478,864MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS028095.1:778,112–826,084MAT1-1MAT1-1-1, MAT1-2-1, APN2, SLA20fewer than 2 genes could be modelled
MATDS028100.1:371,587–416,014MAT1-2APN2, SLA2, CIMG_004070fewer than 2 genes could be modelled
MATDS028103.1:359,874–402,836MAT1-1MAT1-1-1, APN2, MAT1-1-30fewer than 2 genes could be modelled

Provenance

Genome file
CimmitisRMSCC2394.genome.fasta
Assembly
31 contigs · 28.9 Mb · N50 3.6 Mb
Genome SHA-256
b32bcfe1c9a6aad8a4932250c20794799d8411ed24dca7175a50a1c4556b1ebf
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': [], '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
2026-11-07T01:48:02Z
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