MATPredict · mating-type report

CposadasiiCPA0066

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 02:03 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 DS562368.1MAT1-2 locus: genes from left to right on DS562368.1, 23,879 to 36,115: SLA2 (conserved flank, plus strand); CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).24 kb26 kb28 kb30 kb32 kb34 kb36 kb← 23.3 kb more to contig endcalled locusSLA2: conserved flank, 23,879–27,668 (+), identity 99.12%, gene modelSLA2CIMG_00407: core MAT gene, 29,587–30,480 (-), identity 99.23%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 29,720–29,842 (-), identity 34.146%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 31,164–31,280 (+), identity 35.897%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 31,643–32,026 (+), identity 99.22%, the two modelling tools disagreeMAT1-2-1APN2: conserved flank, 32,764–34,817 (-), identity 98.16%, the two modelling tools disagreeAPN2COX13: conserved flank, 35,450–36,115 (+), identity 98.48%, gene modelCOX13
Gene order on DS562368.1. 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
DS562368.1:23,879–36,115 · 12.2 kb
Own genes
DS562368.1:23,879–36,115 · 12.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
23.9 kb
Region (samtools)
DS562368.1:23879-36115
Idiomorph scores
  • MAT1-2 398.0

Margin over the set-aside MAT1-1-3 hit: 62.3 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
MAT1-2-198.2MAT1-1-335.9100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankgene modelexonerate3 frameshiftsdefective gene model99.1cov 98.1%< 1e-180867 bits23,879–27,668 +115501_rs_MAT_MAT1-2
CIMG_00407core MATgene modelexonerate99.2cov 100.0%1.5e-127398 bits29,587–30,480 -35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn34.1cov 16.0%1.1e-0636 bits29,720–29,842 -–746128_af293_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn35.9cov 23.0%1.6e+0029 bits31,164–31,280 +–5127_mo44_MAT_MAT1-1
MAT1-2-1core MATmodels differexonerateminiprot: 30,925–32,029, 75.3%99.2cov 37.9%2.8e-79263 bits31,643–32,026 +1199306_silveira_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 32,761–34,817, 94.8%98.2cov 100.0%< 1e-1801,072 bits32,764–34,817 -65501_rs_MAT_MAT1-2
COX13conserved flankgene modelexonerate98.5cov 100.0%3.9e-34124 bits35,450–36,115 +55501_rs_MAT_MAT1-2

Withheld candidate loci 9

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

Show the 9 withheld loci

Withheld loci (9)

familylocationidiomorph genesmodelledreason
MATDS562621.1:17,595–40,849MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATDS562414.1:91,290–107,064MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS562478.1:6,985–55,244MAT1-2MAT1-2-1, APN2, SLA2, MAT1-2-40fewer than 2 genes could be modelled
MATDS562443.1:64,583–70,320MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS562530.1:26,309–53,465MAT1-1MAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS562510.1:16,461–31,342MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATDS562426.1:8,736–11,668MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS562553.1:7,444–28,291MAT1-2MAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS562371.1:159,996–160,788MAT1-2MAT1-2-1, MAT1-2-41too few of the family's genes found

Provenance

Genome file
CposadasiiCPA0066.genome.fasta
Assembly
475 contigs · 27.8 Mb · N50 87.5 kb
Genome SHA-256
a2246a18cc2ee2c578e0f43a3878d7cd783c3f5f835d0f6d2e0a4154521b62b9
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
2026-11-07T02:02:51Z
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