MATPredict · mating-type report

EfestucaeFl1

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 02:05 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 CP031390MAT1-2 locus: genes from left to right on CP031390, 1,504,669 to 1,530,187: SLA2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).1,505 kb1,510 kb1,515 kb1,520 kb1,525 kb1,530 kb← 1,503.4 kb more to contig endcalled locusSLA2: conserved flank, 1,511,784–1,515,790 (+), identity 81.86%, gene modelSLA2MAT1-2-1: core MAT gene, 1,525,024–1,525,515 (+), identity 56.72%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 1,525,210–1,525,482 (+), identity 28.571%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)APN2: conserved flank, 1,527,505–1,528,734 (-), identity 71.66%, the two modelling tools disagreeAPN2COX13: conserved flank, 1,529,497–1,530,187 (+), identity 69.91%, the two modelling tools disagreeCOX13
Gene order on CP031390. 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
CP031390:1,504,669–1,530,187 · 25.5 kb
Own genes
CP031390:1,511,784–1,530,187 · 18.4 kb · the span runs 7.1 kb beyond these genes
Supported span
CP031390:1,511,781–1,530,187 · 18.4 kb · 7.1 kb of the reported span rests only on hits below 33 bits
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
1.5 Mb
Region (samtools)
CP031390:1504669-1530187
Idiomorph scores
  • MAT1-2 137.0

Margin over the set-aside MAT1-1-3 hit: 18.4 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
MAT1-2-147.0MAT1-1-328.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankgene modelexonerate81.9cov 100.0%< 1e-1801,308 bits1,511,784–1,515,790 +4578113_sxlc146_MAT_MAT1-2
MAT1-2-1core MATmodels differexonerateminiprot: 1,524,910–1,525,515, 50.3%56.7cov 61.0%4.2e-37137 bits1,525,024–1,525,515 +35127_mo45_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn28.6cov 42.0%5.1e-0748 bits1,525,210–1,525,482 +–230073_uamh-1363_MAT_MAT1-1
APN2conserved flankmodels differexonerateminiprot: 1,526,595–1,528,891, 51.0%71.7cov 66.9%< 1e-180580 bits1,527,505–1,528,734 -327337_vdls-17_MAT_MAT1-2
COX13conserved flankmodels differexonerateminiprot: 1,529,471–1,530,190, 66.4%69.9cov 88.5%2.0e-2189 bits1,529,497–1,530,187 +3578113_sxlc146_MAT_MAT1-2

Withheld candidate loci 11

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).

Show the 11 withheld loci

Withheld loci (11)

familylocationidiomorph genesmodelledreason
MATCP031390:3,118,943–3,126,163MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP031386:1,791,235–1,815,362MAT1-1MAT1-1-1, APN2, COX130fewer than 2 genes could be modelled
MATCP031386:3,410,982–3,419,593MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATCP031386:4,234,809–4,254,589MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATCP031386:4,402,079–4,422,049MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP031385:4,732,430–4,744,922MAT1-1APN2, COX13, MAT1-1-20fewer than 2 genes could be modelled
MATCP031385:5,560,284–5,578,278MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATCP031387:1,568,873–1,578,638MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP031387:2,713,824–2,732,725MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATCP031387:3,882,722–3,908,274MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATCP031388:458,932–476,432MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled

Provenance

Genome file
EfestucaeFl1.genome.fasta
Assembly
8 contigs · 35.0 Mb · N50 6.2 Mb
Genome SHA-256
6c5cc67156d4c95c7191d0fb795c17df5e4a59231404491810ecaa3f411ac9bd
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': 34397, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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
2026-11-07T02:04:32Z
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