MATPredict · mating-type report

PgraminisCRL75-36-700-3

MAT locus above the FungiDB annotation (gene by gene)

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 02:02 UTC by MATPredict 0.8.1

Result

Mating type

undeterminedhigh confidence

Called loci 1

undetermined rustHD family · Basidiomycota

high confidence
Gene order of the undetermined locus on DS178274undetermined locus: genes from left to right on DS178274, 405,328 to 409,148: bE (core MAT gene, minus strand); bW (core MAT gene, plus strand).406 kb407 kb408 kb409 kb← 405.0 kb more to contig endcalled locusbE: core MAT gene, 405,328–406,672 (-), identity 100.0%, search hit onlybEbW: core MAT gene, 407,218–409,148 (+), identity 100.0%, search hit onlybW
Gene order on DS178274. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on DS178274, 405,028 to 409,448PGTG_05143 405,310-406,857 (-): hypothetical proteinPGTG_05143PGTG_05144 407,104-409,148 (+): hypothetical proteinPGTG_05144
FungiDB release 68 annotation of the same window: gene models from the GFF (filled = CDS, pale = UTR exon, line = intron, arrow = strand). Green genes overlap a MATPredict gene on the same strand; grey genes do not. Click a gene to open it on fungidb.org.
  • core MAT gene
  • search hit only
  • Idiomorph undetermined: the evidence for two idiomorphs is tied or too close to call.
Location
DS178274:405,328–409,148 · 3.8 kb
Own genes
DS178274:405,328–409,148 · 3.8 kb
Locus
A MAT gene with no flanking gene beside it; not a full locus.
Genes modelled
2 of 2 gene hits
Nearest contig end
405.3 kb
Region (samtools)
DS178274:405328-409148

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
bEcore MAThit onlyDIAMOND, proteome100.0cov 100.0%1.1e-227616 bits405,328–406,672 -–418459_crl-75-36-700-3_rustHD_b1PGTG_05143
bWcore MAThit onlyDIAMOND, proteome100.0cov 100.0%< 1e-180934 bits407,218–409,148 +–418459_crl-75-36-700-3_rustHD_b1PGTG_05144

Withheld candidate loci 8

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).

Show the 8 withheld loci

Withheld loci (8)

familylocationidiomorph genesmodelledreason
rustHDDS178274:282,701–284,192undeterminedbE1fewer than 2 genes could be modelled
rustHDDS178262:1,611,889–1,611,978undeterminedbW0fewer than 2 genes could be modelled
rustHDDS990023:395–592undeterminedbW0fewer than 2 genes could be modelled
rustHDDS178357:167,878–168,045undeterminedbW0fewer than 2 genes could be modelled
rustHDDS178272:1,053,648–1,053,863undeterminedbW0fewer than 2 genes could be modelled
rustHDDS178392:96,488–96,595undeterminedbW0fewer than 2 genes could be modelled
rustHDDS178268:1,466,204–1,466,407undeterminedbW0fewer than 2 genes could be modelled
rustHDDS178327:271,439–271,630undeterminedbW0fewer than 2 genes could be modelled

Provenance

Genome file
PgraminisCRL75-36-700-3.genome.fasta
Assembly
393 contigs · 88.7 Mb · N50 965.0 kb
Genome SHA-256
e0f8ac02b23768daaab3755d9d87c3d9030011af6f033c38051900103546752a
MATPredict
0.8.1 (v0.8.1, 3a62e6302b)
Database
86f18d232e4fe95d · 185 records
Taxonomy
local NCBI taxonomy snapshot 2026-10-01
Parameters
phylum=Basidiomycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Basidiomycota', 'phylum_taxid': 5204, 'deepest_rank': 'genus', 'routing_taxid': 5262, '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 Basidiomycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 5262', 'routed_by': 'family taxid 5262 (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, supported_min_bitscore=33.0
Run started
2026-11-07T02:02:03Z
Run time
41 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