MATPredict · mating-type report

CposadasiiRMSCC1038

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 02:26 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 DS560902.1MAT1-2 locus: genes from left to right on DS560902.1, 7,122 to 19,354: 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).8 kb10 kb12 kb14 kb16 kb18 kb← 6.5 kb more to contig endcalled locusCOX13: conserved flank, 7,122–7,788 (-), identity 98.48%, the two modelling tools disagreeCOX13APN2: conserved flank, 8,417–10,470 (+), identity 98.16%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 11,548–12,320 (-), identity 97.71%, gene modelMAT1-2-1MAT1-1-3: core MAT gene, 11,590–12,081 (-), identity 26.829%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)CIMG_00407: core MAT gene, 12,765–13,658 (+), identity 99.23%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 13,403–13,525 (+), identity 34.146%, search hit onlyMAT1-2-4SLA2: conserved flank, 15,421–19,354 (-), identity 99.81%, gene modelSLA2
Gene order on DS560902.1. 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
DS560902.1:7,122–19,354 · 12.2 kb
Own genes
DS560902.1:7,122–19,354 · 12.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
7.1 kb
Region (samtools)
DS560902.1:7122-19354
Idiomorph scores
  • MAT1-2 398.0

Margin over the set-aside MAT1-1-3 hit: 59.7 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
MAT1-2-186.5MAT1-1-326.8100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankmodels differexonerateminiprot: 7,119–7,788, 86.4%98.5cov 100.0%2.7e-67219 bits7,122–7,788 -55501_rs_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 8,417–10,473, 94.8%98.2cov 100.0%< 1e-1801,071 bits8,417–10,470 +65501_rs_MAT_MAT1-2
MAT1-2-1core MATgene modelexonerate97.7cov 65.1%3.5e-118315 bits11,548–12,320 -3199306_silveira_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn26.8cov 86.0%2.2e-0852 bits11,590–12,081 -–5127_mo44_MAT_MAT1-1
CIMG_00407core MATgene modelexonerate99.2cov 100.0%1.3e-127398 bits12,765–13,658 +35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn34.1cov 16.0%1.1e-0636 bits13,403–13,525 +–746128_af293_MAT_MAT1-2
SLA2conserved flankgene modelexonerate1 frameshiftdefective gene model99.8cov 100.0%< 1e-180911 bits15,421–19,354 -125501_rs_MAT_MAT1-2

Withheld candidate loci 13

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

Show the 13 withheld loci

Withheld loci (13)

familylocationidiomorph genesmodelledreason
MATDS560970.1:16,176–16,746MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATDS560758.1:40,386–65,520undeterminedAPN2, SLA2, COX130fewer than 2 genes could be modelled
MATDS560692.1:13,630–53,266MAT1-1MAT1-1-1, SLA2, MAT1-1-40fewer than 2 genes could be modelled
MATDS560825.1:18,240–40,081MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS560844.1:32,551–50,851MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATDS560711.1:38,342–53,574MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS560793.1:12,034–36,443MAT1-2MAT1-2-1, SLA2, MAT1-2-40fewer than 2 genes could be modelled
MATDS560674.1:36,852–56,993MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS560826.1:32,531–34,385MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS560780.1:9,147–14,831MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS560837.1:8,769–11,791MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS560975.1:5,218–6,860MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS560892.1:13,869–14,652MAT1-2MAT1-2-1, MAT1-2-41too few of the family's genes found

Provenance

Genome file
CposadasiiRMSCC1038.genome.fasta
Assembly
554 contigs · 26.2 Mb · N50 77.2 kb
Genome SHA-256
fce5accdc597f22fcbc6b826523317084a6f6e359b32ce25b55ede5edab9a00b
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
2026-11-07T02:25:45Z
Run time
56 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