MATPredict · mating-type report

CposadasiiRMSCC3700

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 02:29 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 DS544250.1MAT1-2 locus: genes from left to right on DS544250.1, 865,822 to 878,033: 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).866 kb868 kb870 kb872 kb874 kb876 kb878 kb429.8 kb more to contig end →called locusCOX13: conserved flank, 865,822–866,488 (-), identity 98.48%, gene modelCOX13APN2: conserved flank, 867,117–869,170 (+), identity 98.32%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 869,909–870,670 (-), identity 99.15%, gene modelMAT1-2-1MAT1-1-3: core MAT gene, 870,332–870,658 (-), identity 26.606%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)CIMG_00407: core MAT gene, 871,546–872,337 (+), identity 93.39%, the two modelling tools disagreeCIMG_00407MAT1-2-4: core MAT gene, 872,082–872,204 (+), identity 34.146%, search hit onlyMAT1-2-4SLA2: conserved flank, 874,100–878,033 (-), identity 99.71%, gene modelSLA2
Gene order on DS544250.1. 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
DS544250.1:865,822–878,033 · 12.2 kb
Own genes
DS544250.1:865,822–878,033 · 12.2 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
430.4 kb
Region (samtools)
DS544250.1:865822-878033
Idiomorph scores
  • MAT1-2 480.0

Margin over the set-aside MAT1-1-3 hit: 65.9 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
MAT1-2-192.5MAT1-1-326.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankgene modelexonerate1 frameshiftdefective gene model98.5cov 100.0%1.3e-29111 bits865,822–866,488 -55501_rs_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 867,117–869,173, 95.0%98.3cov 100.0%< 1e-1801,073 bits867,117–869,170 +65501_rs_MAT_MAT1-2
MAT1-2-1core MATgene modelexonerate99.2cov 69.8%7.1e-155480 bits869,909–870,670 -2199306_silveira_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn26.6cov 51.0%6.8e-0954 bits870,332–870,658 -–230073_uamh-1363_MAT_MAT1-1
CIMG_00407core MATmodels differexonerateminiprot: 871,574–872,340, 97.3%1 internal stopdefective gene model93.4cov 87.1%4.8e-91293 bits871,546–872,337 +35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn34.1cov 16.0%8.9e-0736 bits872,082–872,204 +–746128_af293_MAT_MAT1-2
SLA2conserved flankgene modelexonerate99.7cov 100.0%< 1e-180911 bits874,100–878,033 -125501_rs_MAT_MAT1-2

Withheld candidate loci 12

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

Show the 12 withheld loci

Withheld loci (12)

familylocationidiomorph genesmodelledreason
MATDS544250.1:324,686–338,397MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS544250.1:1,079,417–1,103,710MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS544293.1:178,487–190,945MAT1-1MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS544266.1:269,403–290,471MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS544298.1:88,582–111,200MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS544277.1:67,679–75,698MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS544279.1:200,570–226,149MAT1-1MAT1-1-1, APN2, MAT1-1-2, MAT1-1-50fewer than 2 genes could be modelled
MATDS544340.1:52,465–70,792MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATDS544256.1:301,995–326,276MAT1-2MAT1-2-1, SLA2, MAT1-2-40fewer than 2 genes could be modelled
MATDS544272.1:123,465–139,509MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS544304.1:120,120–134,983MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATDS544259.1:254,357–255,149MAT1-2MAT1-2-1, MAT1-2-41too few of the family's genes found

Provenance

Genome file
CposadasiiRMSCC3700.genome.fasta
Assembly
243 contigs · 25.5 Mb · N50 284.7 kb
Genome SHA-256
00b91d42ac33c9457850ef98189217d796bf01a9bbe940848cddd0f77c55326f
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
2026-11-07T02:28:33Z
Run time
49 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