MATPredict · mating-type report

CqueenslandicumCBS280.77

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 01:55 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 LJPI01001015.1MAT1-2 locus: genes from left to right on LJPI01001015.1, 169,469 to 181,148: 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).170 kb172 kb174 kb176 kb178 kb180 kb162.7 kb more to contig end →called locusCOX13: conserved flank, 169,469–170,120 (-), identity 87.69%, gene modelCOX13APN2: conserved flank, 170,508–171,893 (+), identity 78.19%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 173,270–174,436 (-), identity 70.45%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 173,741–174,016 (-), identity 30.435%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)CIMG_00407: core MAT gene, 174,865–175,744 (+), identity 65.75%, gene modelCIMG_00407MAT1-2-4: core MAT gene, 175,126–175,395 (+), identity 22.222%, search hit onlyMAT1-2-4SLA2: conserved flank, 177,242–181,148 (-), identity 97.9%, gene modelSLA2
Gene order on LJPI01001015.1. 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
LJPI01001015.1:169,469–181,148 · 11.7 kb
Own genes
LJPI01001015.1:169,469–181,148 · 11.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
163.2 kb
Region (samtools)
LJPI01001015.1:169469-181148
Idiomorph scores
  • MAT1-2 458.0

Margin over the set-aside MAT1-1-3 hit: 32.4 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
MAT1-2-162.9MAT1-1-330.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankgene modelexonerate87.7cov 97.8%6.7e-36122 bits169,469–170,120 -45501_rs_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 170,508–172,490, 66.9%78.2cov 63.2%< 1e-180674 bits170,508–171,893 +65501_rs_MAT_MAT1-2
MAT1-2-1core MATmodels differexonerateminiprot: 173,267–174,436, 65.5%70.5cov 100.0%4.5e-147458 bits173,270–174,436 -45501_rs_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn30.4cov 41.0%3.9e-0955 bits173,741–174,016 -–230073_uamh-1363_MAT_MAT1-1
CIMG_00407core MATgene modelexonerate65.8cov 98.5%1.2e-88237 bits174,865–175,744 +35501_rs_MAT_MAT1-2
MAT1-2-4core MAThit onlytblastn22.2cov 36.0%4.1e-0132 bits175,126–175,395 +–746128_af293_MAT_MAT1-2
SLA2conserved flankgene modelexonerate97.9cov 100.0%< 1e-180936 bits177,242–181,148 -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 (13).

Show the 13 withheld loci

Withheld loci (13)

familylocationidiomorph genesmodelledreason
MATLJPI01001372.1:228,182–237,803MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPI01000097.1:118,372–163,752MAT1-1MAT1-1-1, COX13, MAT1-1-3, MAT1-1-50fewer than 2 genes could be modelled
MATLJPI01000351.1:53,446–81,587MAT1-2APN2, SLA2, MAT1-2-100fewer than 2 genes could be modelled
MATLJPI01001260.1:286,015–287,364MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPI01000852.1:6,929–8,709MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPI01000859.1:420,977–429,435MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLJPI01000122.1:10,797–14,037MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLJPI01000533.1:27,235–58,036MAT1-2MAT1-2-1, COX13, MAT1-2-100fewer than 2 genes could be modelled
MATLJPI01000981.1:279,546–281,625MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLJPI01000281.1:283,285–298,167MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPI01000627.1:113,708–115,957MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPI01001055.1:5,057–26,131MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLJPI01000166.1:22,367–27,970MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled

Provenance

Genome file
CqueenslandicumCBS280.77.genome.fasta
Assembly
2,724 contigs · 32.3 Mb · N50 173.8 kb
Genome SHA-256
4f69b825c9728d2cd09c56247dc1b514153e5af98874949ac7f16c5fbc56aec0
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
2026-11-07T01:54:13Z
Run time
81 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