AoryzaeRIB40 – MATPredict report

Result

Mating type

MAT1-1: complete locus, high confidence, 10.8 kb on Chr6_A_oryzae_RIB40. Gene order: APN2 · MAT1-1-1 · SLA2.

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence

Gene order on Chr6_A_oryzae_RIB40. Scroll sideways to see the whole figure.

FungiDB release 71 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

MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.

Location: Chr6_A_oryzae_RIB40:1,576,032–1,586,821 · 10.8 kb
Own genes: Chr6_A_oryzae_RIB40:1,576,032–1,586,821 · 10.8 kb
Locus: Complete locus: MAT gene(s) with their flanking genes.
Genes modelled: 3 of 4 gene hits
Nearest contig end: 1.6 Mb
Region (samtools): Chr6_A_oryzae_RIB40:1576032-1586821

Idiomorph scores

MAT1-1 376.0
MAT1-2 29.6

Margin over the next idiomorph: 346.4

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

Gene	Role	Model	Identity %	E-value	Position (strand)	Exons	Reference record	FungiDB gene
APN2	conserved flank	hit onlyDIAMOND, proteome	84.1cov 36.7%	9.2e-321876 bits	1,576,032–1,578,187 +	–	2903220_liq80xsp_MAT_combined	AO090020000091
MAT1-2-1	core MATother idiomorph, not counted	hit onlytblastn	34.1cov 12.0%	4.7e+0030 bits	1,576,429–1,576,560 +	–	5141_unknown-1_MAT_MAT1-2	AO090020000091
MAT1-1-1	core MAT	hit onlyDIAMOND, proteome	53.8cov 100.0%	2.6e-132376 bits	1,579,999–1,581,166 +	–	746128_a1163_MAT_MAT1-1	AO090020000089
SLA2	conserved flank	hit onlyDIAMOND, proteome	88.7cov 100.0%	< 1e-1801,631 bits	1,582,726–1,586,821 -	–	746128_af293_MAT_MAT1-2	AO090020000087 end4
COX13	expected, not found							–

What was searched

Routing: By taxonomy. The genome's taxonomy falls inside a curated family's scope; only those families were searched.
Families searched: Ascomycota:MAT
Genetic code: 1
Taxonomy: local NCBI taxonomy snapshot 2026-10-01

Withheld candidate loci 2

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 (2).

Show the 2 withheld loci

Withheld loci (2)

family	location	idiomorph	genes	modelled	reason
MAT	Chr1_A_oryzae_RIB40:1,181,454–1,183,057	MAT1-2	MAT1-2-1	1	too few of the family's genes found
MAT	Chr2_A_oryzae_RIB40:5,184,090–5,186,301	MAT1-2	MAT1-2-1	1	too few of the family's genes found

Provenance

Genome file: AoryzaeRIB40.genome.fasta
Assembly: 12 contigs · 37.9 Mb · N50 4.9 Mb
Genome SHA-256: 676332773ad0457a2a73a9df3c65c21a5e3d66219108db1eb3ff37e2d45403f9
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': 1131492, '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 1131492', 'routed_by': 'family taxid 1131492 (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: 2026-11-07T02:27:54Z
Run time: 84 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

MATPredict reads an assembly; it is not a mating assay. Two idiomorphs in one assembly can come from a homothallic species, a mixed culture or a merged diploid assembly.
Fragmented assemblies can split a locus or lose its flanking genes; an uncalled genome is weak evidence of absence.
Lineages with no curated record are searched with the whole phylum's references; family labels there are less reliable.