MATPredict · mating-type report

Fgraminearum233423

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 01:52 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-1high confidenceMAT1-1medium confidence

Called loci 2

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on LAJZ01000089MAT1-1 locus: genes from left to right on LAJZ01000089, 54 to 15,402: MAT1-1-3 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, plus strand); MAT1-2-7 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, minus strand); SLA2 (conserved flank, minus strand).5 kb10 kb15 kbcontig endcalled locusMAT1-1-3: core MAT gene, 54–173 (-), identity 97.5%, gene modelMAT1-1-3MAT1-1-2: core MAT gene, 680–2,257 (+), identity 100.0%, the two modelling tools disagreeMAT1-1-2MAT1-1-1: core MAT gene, 2,896–3,983 (+), identity 100.0%, gene modelMAT1-1-1MAT1-2-7: core MAT gene, 3,153–3,368 (+), identity 28.205%, search hit onlyMAT1-2-7 (lost to MAT1-1-1)MAT1-2-1: core MAT gene, 4,615–5,476 (-), identity 100.0%, the two modelling tools disagreeMAT1-2-1SLA2: conserved flank, 11,926–15,390 (-), identity 84.2%, gene modelSLA2
Gene order on LAJZ01000089. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
  • search hit only
Location
LAJZ01000089:54–15,402 · 15.3 kb
Own genes
LAJZ01000089:54–15,390 · 15.3 kb · the span runs 12 bp beyond these genes
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 6 gene hits
Nearest contig end
53 bp
Region (samtools)
LAJZ01000089:54-15402
Idiomorph scores
  • MAT1-1 676.0
  • MAT1-2 380.0

Margin over the next idiomorph: 296.0

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
MAT1-1-199.3MAT1-2-728.2100.0higher identity
MAT1-2-191.6MAT1-1-334.5100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
MAT1-1-3core MATgene modelexonerate97.5cov 22.1%1.2e-1883 bits54–173 -15518_3639_MAT_combined
MAT1-1-2core MATmodels differexonerateminiprot: 680–2,260, 97.1%100.0cov 100.0%< 1e-180676 bits680–2,257 +55518_3639_MAT_combined
MAT1-1-1core MATgene modelexonerate100.0cov 100.0%< 1e-180581 bits2,896–3,983 +25518_3639_MAT_combined
MAT1-2-7core MATlost to MAT1-1-1, not countedhit onlytblastn28.2cov 39.0%5.9e-0234 bits3,153–3,368 +–5158_cbs114723_MAT_unswitched
MAT1-2-1core MATmodels differexonerateminiprot: 4,612–5,476, 93.7%100.0cov 100.0%4.0e-142380 bits4,615–5,476 -35518_3639_MAT_combined
SLA2conserved flankgene modelexonerate84.2cov 99.8%< 1e-1801,296 bits11,926–15,390 -4578113_sxlc146_MAT_MAT1-2
APN2expected, not found
COX13expected, not found

MAT1-1 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-1 locus on LAJZ01000088MAT1-1 locus: genes from left to right on LAJZ01000088, 70,166 to 75,062: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand).70 kb71 kb72 kb73 kb74 kb75 kbcontig endcalled locusCOX13: conserved flank, 70,166–70,899 (-), identity 66.96%, the two modelling tools disagreeCOX13APN2: conserved flank, 71,556–72,823 (+), identity 70.91%, the two modelling tools disagreeAPN2MAT1-1-3: core MAT gene, 74,533–75,062 (-), identity 98.59%, gene modelMAT1-1-3MAT1-2-1: core MAT gene, 74,548–74,811 (-), identity 34.091%, search hit onlyMAT1-2-1 (lost to MAT1-1-3)
Gene order on LAJZ01000088. 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
LAJZ01000088:70,166–75,062 · 4.9 kb
Own genes
LAJZ01000088:70,166–75,062 · 4.9 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
3 of 4 gene hits
Nearest contig end
2 bp
Region (samtools)
LAJZ01000088:70166-75062
Idiomorph scores
  • MAT1-1 198.0

Margin over the set-aside MAT1-2-1 hit: 50.4 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
MAT1-1-384.5MAT1-2-134.1100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
COX13conserved flankmodels differexonerateminiprot: 70,163–70,884, 60.5%67.0cov 88.5%1.3e-2498 bits70,166–70,899 -5578113_sxlc146_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 71,446–73,705, 52.4%1 internal stopdefective gene model70.9cov 70.2%8.2e-175535 bits71,556–72,823 +327337_vdls-17_MAT_MAT1-2
MAT1-1-3core MATgene modelexonerate98.6cov 79.6%2.1e-73198 bits74,533–75,062 -35518_3639_MAT_combined
MAT1-2-1core MATother idiomorph, not countedlost to MAT1-1-3, not countedhit onlytblastn34.1cov 21.0%4.3e-1266 bits74,548–74,811 -–13684_sn436ga98_MAT_MAT1-2
MAT1-1-1expected, not found
SLA2expected, not found

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 (9); too few of the family's genes found (2).

Show the 11 withheld loci

Withheld loci (11)

familylocationidiomorph genesmodelledreason
MATLAJZ01000225:1,739–30,733MAT1-2MAT1-2-1, APN2, SLA20fewer than 2 genes could be modelled
MATLAJZ01000007:249,982–252,033MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLAJZ01000005:483,180–511,891MAT1-2MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATLAJZ01000070:60,357–78,440MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATLAJZ01000079:74,210–82,664MAT1-1MAT1-1-1, APN2, SLA20fewer than 2 genes could be modelled
MATLAJZ01000275:80,981–87,891MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATLAJZ01000208:119,376–122,156MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATLAJZ01000069:21,331–31,216MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLAJZ01000792:179,784–187,970MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATLAJZ01000166:273,993–287,394MAT1-2MAT1-1-1, MAT1-2-11too few of the family's genes found
MATLAJZ01000558:57,689–94,012MAT1-2MAT1-1-1, MAT1-2-1, MAT1-1-51too few of the family's genes found

Provenance

Genome file
Fgraminearum233423.genome.fasta
Assembly
869 contigs · 36.5 Mb · N50 168.0 kb
Genome SHA-256
4a8143f924a52571778fe604ff927ae8109daeb9a650f9708bf3411e13007844
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': 110618, '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 110618', 'routed_by': 'family taxid 110618 (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
2026-11-07T01:50:57Z
Run time
79 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