MATPredict · mating-type report

RlauricolaRL4

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 01:52 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 JACBXF010000158MAT1-2 locus: genes from left to right on JACBXF010000158, 104,782 to 134,183: APN2 (conserved flank, plus strand); COX13 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-1 (core MAT gene, plus strand); SLA2 (conserved flank, minus strand).105 kb110 kb115 kb120 kb125 kb130 kb135 kb← 103.3 kb more to contig endcalled locusAPN2: conserved flank, 104,782–107,359 (+), identity 60.9%, search hit onlyAPN2COX13: conserved flank, 111,228–111,840 (+), identity 74.5%, search hit onlyCOX13MAT1-1-3: core MAT gene, 122,384–123,426 (-), identity 29.2%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 122,384–123,426 (-), identity 57.1%, search hit onlyMAT1-2-1MAT1-1-1: core MAT gene, 125,933–126,713 (+), identity 33.0%, search hit onlyMAT1-1-1SLA2: conserved flank, 130,793–134,183 (-), identity 89.5%, search hit onlySLA2
Gene order on JACBXF010000158. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on JACBXF010000158, 103,311 to 135,655RL4_JR_09417 103,175-104,257 (-): unspecified productRL4_JR_09417RL4_JR_09418 104,782-107,359 (+): unspecified productRL4_JR_09418RL4_JR_09419 107,696-109,551 (-): unspecified productRL4_JR_09419RL4_JR_09420 111,228-111,840 (+): unspecified productRL4_JR_09420RL4_JR_09421 113,048-113,236 (+): unspecified productRL4_JR_09421RL4_JR_09422 122,384-123,426 (-): unspecified productRL4_JR_09422RL4_JR_09423 125,933-126,713 (+): unspecified productRL4_JR_09423RL4_JR_09424 127,067-127,753 (+): unspecified productRL4_JR_09424RL4_JR_09425 128,366-129,232 (+): unspecified productRL4_JR_09425RL4_JR_09426 130,793-134,183 (-): unspecified productRL4_JR_09426RL4_JR_09427 134,684-139,354 (+): unspecified productRL4_JR_09427
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
Location
JACBXF010000158:104,782–134,183 · 29.4 kb
Own genes
JACBXF010000158:104,782–134,183 · 29.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
5 of 6 gene hits
Nearest contig end
104.8 kb
Region (samtools)
JACBXF010000158:104782-134183
Idiomorph scores
  • MAT1-2 296.0
  • MAT1-1 68.9

Margin over the next idiomorph: 227.1

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
MAT1-2-157.1MAT1-1-329.2100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
APN2conserved flankhit onlyDIAMOND, proteome60.9cov 84.0%1.3e-128390 bits104,782–107,359 +–1301501_voucher-267_MAT_MAT1-2RL4_JR_09418
COX13conserved flankhit onlyDIAMOND, proteome74.5cov 67.1%4.4e-44134 bits111,228–111,840 +–199306_rmscc1040_MAT_MAT1-1RL4_JR_09420
MAT1-1-3core MATlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome29.2cov 61.7%2.5e-1463 bits122,384–123,426 -–230073_uamh-1363_MAT_MAT1-1RL4_JR_09422
MAT1-2-1core MAThit onlyDIAMOND, proteome57.1cov 98.5%1.8e-103296 bits122,384–123,426 -–230073_uamh-11059_MAT_MAT1-2RL4_JR_09422
MAT1-1-1core MAThit onlyDIAMOND, proteome33.0cov 22.2%6.1e-1669 bits125,933–126,713 +–230073_uamh-1363_MAT_MAT1-1RL4_JR_09423
SLA2conserved flankhit onlyDIAMOND, proteome89.5cov 100.0%< 1e-1801,191 bits130,793–134,183 -–230073_uamh-1363_MAT_MAT1-1RL4_JR_09426

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATJACBXF010000010:721,940–724,968MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
RlauricolaRL4.genome.fasta
Assembly
169 contigs · 34.6 Mb · N50 3.1 Mb
Genome SHA-256
7f2bcb05a4a651940f1f19a4d43335304097acb784700cac8c69064cad073452
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': 5152, '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 5152', 'routed_by': 'family taxid 5152 (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
2026-11-07T01:51:20Z
Run time
80 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