MATPredict · mating-type report

Poryzae70-15

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 01:54 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 CM001237MAT1-2 locus: genes from left to right on CM001237, 764,489 to 780,039: COX13 (conserved flank, plus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand).765 kb770 kb775 kb780 kb← 763.7 kb more to contig endcalled locusCOX13: conserved flank, 764,489–765,597 (+), identity 67.5%, search hit onlyCOX13APN2: conserved flank, 774,003–776,369 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 778,536–780,039 (-), identity 35.6%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 778,536–780,039 (-), identity 53.8%, search hit onlyMAT1-2-1
Gene order on CM001237. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CM001237, 763,712 to 780,815MGG_17900 760,520-764,159 (+): RING-9 proteinMGG_17900MGG_17901 764,269-766,588 (+): Cytochrome c oxidase subunit ViaMGG_17901MGG_17902 766,305-766,930 (-): hypothetical proteinMGG_17902MGG_02982 767,834-770,070 (+): averantin oxidoreductaseMGG_02982MGG_02981 770,307-773,575 (-): anaphase-promoting complex proteinMGG_02981MGG_02980 772,852-776,683 (+): DNA-(apurinic or apyrimidinic site) lyase 2MGG_02980MGG_02979 777,046-778,251 (-): hypothetical proteinMGG_02979 MAT1-1MGG_02978 778,536-780,039 (-): mating-type protein mat a-1MGG_02978
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
  • conserved flank
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CM001237:764,489–780,039 · 15.6 kb
Own genes
CM001237:764,489–780,039 · 15.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 4 gene hits
Nearest contig end
764.5 kb
Region (samtools)
CM001237:764489-780039
Idiomorph scores
  • MAT1-2 109.0

Margin over the set-aside MAT1-1-3 hit: 18.2 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
MAT1-2-153.8MAT1-1-335.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome67.5cov 92.3%1.3e-59173 bits764,489–765,597 +–578113_sxlc146_MAT_MAT1-2MGG_17901
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%3.3e-236662 bits774,003–776,369 +–2903220_liq80xsp_MAT_combinedMGG_02980
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome35.6cov 45.1%2.0e-1258 bits778,536–780,039 -–5127_mo44_MAT_MAT1-1MGG_02978
MAT1-2-1core MAThit onlyDIAMOND, proteome53.8cov 73.8%5.8e-29109 bits778,536–780,039 -–61372_suf959_MAT_MAT1-2MGG_02978
SLA2expected, not found–

Withheld candidate loci 3

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: too few of the family's genes found (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATCM001231:5,938,304–5,963,516MAT1-2MAT1-2-1, MAT1-1-51too few of the family's genes found
MATCM001236:2,427,237–2,429,807MAT1-2MAT1-2-11too few of the family's genes found
MATCM001237:864,578–887,741MAT1-1SLA2, MAT1-1-21too few of the family's genes found

Provenance

Genome file
Poryzae70-15.genome.fasta
Assembly
53 contigs · 41.0 Mb · N50 6.6 Mb
Genome SHA-256
33628aeac6f683dfe60de18013b2b672d0865aea63dd3421b8018dd1617e449e
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': 2528436, '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 2528436', 'routed_by': 'family taxid 2528436 (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
2026-11-07T01:52:53Z
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