MATPredict · mating-type report

EglyceriaeE277

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 02:07 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on AFRG01000185MAT1-1 locus: genes from left to right on AFRG01000185, 3,632 to 23,479: 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); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).5 kb10 kb15 kb20 kbcontig endcalled locusCOX13: conserved flank, 3,632–4,296 (-), identity 69.91%, the two modelling tools disagreeCOX13APN2: conserved flank, 5,051–7,187 (+), identity 53.38%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 8,049–8,435 (-), identity 33.571%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)MAT1-1-3: core MAT gene, 8,070–8,730 (-), identity 46.43%, gene modelMAT1-1-3MAT1-1-2: core MAT gene, 9,490–9,966 (+), identity 37.74%, gene modelMAT1-1-2MAT1-1-1: core MAT gene, 11,107–11,651 (+), identity 48.75%, the two modelling tools disagreeMAT1-1-1SLA2: conserved flank, 19,448–23,476 (-), identity 81.77%, gene modelSLA2
Gene order on AFRG01000185. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
AFRG01000185:3,632–23,479 · 19.8 kb
Own genes
AFRG01000185:3,632–23,476 · 19.8 kb · the span runs 3 bp beyond these genes
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
6 of 7 gene hits
Nearest contig end
3.6 kb
Region (samtools)
AFRG01000185:3632-23479
Idiomorph scores
  • MAT1-1 165.0

Margin over the set-aside MAT1-2-1 hit: 9.5 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
MAT1-1-343.1MAT1-2-133.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankmodels differexonerateminiprot: 3,629–4,335, 63.9%69.9cov 88.5%1.4e-2189 bits3,632–4,296 -3578113_sxlc146_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 4,896–7,190, 50.9%53.4cov 97.1%< 1e-180578 bits5,051–7,187 +4746128_a1163_MAT_MAT1-1
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn33.6cov 33.0%1.1e-1064 bits8,049–8,435 -–13684_sn436ga98_MAT_MAT1-2
MAT1-1-3core MATgene modelexonerate46.4cov 95.6%8.4e-3595 bits8,070–8,730 -45518_3639_MAT_combined
MAT1-1-2core MATgene modelexonerate37.7cov 39.0%8.0e-38146 bits9,490–9,966 +15127_mo44_MAT_MAT1-1
MAT1-1-1core MATmodels differexonerateminiprot: 10,936–12,041, 34.6%48.8cov 45.4%5.6e-45165 bits11,107–11,651 +259765_880621a-1_MAT_MAT1-1
SLA2conserved flankgene modelexonerate81.8cov 100.0%< 1e-1801,305 bits19,448–23,476 -4578113_sxlc146_MAT_MAT1-2

Withheld candidate loci 10

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 (10).

Show the 10 withheld loci

Withheld loci (10)

familylocationidiomorph genesmodelledreason
MATAFRG01000205:11,094–19,447MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATAFRG01000047:44,814–54,607MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATAFRG01000305:16,965–21,990MAT1-2MAT1-2-1, COX131fewer than 2 genes could be modelled
MATAFRG01000777:9,339–16,380MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATAFRG01000016:23,490–33,160MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATAFRG01000084:58,709–68,138MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATAFRG01000780:812–13,028MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATAFRG01000180:11,709–14,722MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATAFRG01000052:35,337–36,854MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATAFRG01000163:5,034–9,433MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled

Provenance

Genome file
EglyceriaeE277.genome.fasta
Assembly
3,076 contigs · 46.7 Mb · N50 44.8 kb
Genome SHA-256
a2c8c4003356a242f82936e18bddc7b1b30f67f74e9ac8cffe49e12b93dbd14d
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': 34397, 'routing_taxid_rank': 'family', 'flags': [], '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 34397', 'routed_by': 'family taxid 34397 (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
2026-11-07T02:05:55Z
Run time
95 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