MATPredict · mating-type report

Cauris6684

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 02:19 UTC by MATPredict 0.8.1

Result

Mating type

Ahigh confidence

Called loci 1

A MTL family · Ascomycota

high confidence
Gene order of the A locus on LGST01000043A locus: genes from left to right on LGST01000043, 172,813 to 180,175: PAP1 (variable flank, minus strand); OBP1 (variable flank, plus strand); PIK1 (variable flank, plus strand); MTLA2 (core MAT gene, plus strand); MTLA1 (core MAT gene, plus strand).174 kb176 kb178 kb180 kb132.4 kb more to contig end →called locusPAP1: variable flank, 172,813–174,447 (-), identity 100.0%, search hit onlyPAP1OBP1: variable flank, 174,674–175,963 (+), identity 100.0%, search hit onlyOBP1PIK1: variable flank, 176,416–179,253 (+), identity 100.0%, search hit onlyPIK1MTLA2: core MAT gene, 179,339–179,952 (+), identity 98.68%, the two modelling tools disagreeMTLA2MTLA1: core MAT gene, 180,026–180,175 (+), identity 95.7%, search hit onlyMTLA1
Gene order on LGST01000043. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on LGST01000043, 172,445 to 180,543QG37_06421 171,289-172,770 (+): unspecified productQG37_06421QG37_06422 172,813-174,447 (-): pap1QG37_06422QG37_06423 174,674-175,963 (+): obp1QG37_06423QG37_06424 176,416-179,253 (+): pik1QG37_06424QG37_06425 180,026-180,175 (+): unspecified productQG37_06425
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
  • variable flank
  • tools disagree
  • alternate model
  • search hit only
Location
LGST01000043:172,813–180,175 · 7.4 kb
Cross-lineage class
MAT1-2
Own genes
LGST01000043:172,813–180,175 · 7.4 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
132.8 kb
Region (samtools)
LGST01000043:172813-180175
Idiomorph scores
  • A 164.0

No other idiomorph scored.

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
PAP1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,087 bits172,813–174,447 -–498019_b11205_MTL_AQG37_06422
OBP1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%7.0e-322860 bits174,674–175,963 +–498019_b11205_MTL_AQG37_06423
PIK1variable flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,649 bits176,416–179,253 +–498019_b11205_MTL_AQG37_06424
MTLA2core MATmodels differexonerateminiprot: 179,339–179,955, 92.5%98.7cov 100.0%3.2e-48164 bits179,339–179,952 +2498019_b11243_MTL_Anone
MTLA1core MAThit onlyDIAMOND, proteome95.7cov 27.7%2.5e-2891 bits180,026–180,175 +–498019_b11205_MTL_AQG37_06425

Withheld candidate loci 48

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 (47); too few of the family's genes found (1).

Show the 48 withheld loci

Withheld loci (48)

familylocationidiomorph genesmodelledreason
MTLLGST01000007:107,081–125,791AMTLA1, PIK11fewer than 2 genes could be modelled
MTLLGST01000019:66,182–66,319AMTLA10fewer than 2 genes could be modelled
MTLLGST01000018:46,289–71,138alphaMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLLGST01000069:4,199–4,315alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000031:145,599–145,718AMTLA10fewer than 2 genes could be modelled
MTLLGST01000031:223,640–223,765AMTLA20fewer than 2 genes could be modelled
MTLLGST01000031:380,340–380,672AMTLA10fewer than 2 genes could be modelled
MTLLGST01000031:481,649–481,783alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000020:153,635–153,784AMTLA20fewer than 2 genes could be modelled
MTLLGST01000020:299,193–299,372AMTLA10fewer than 2 genes could be modelled
MTLLGST01000023:104,221–104,352AMTLA10fewer than 2 genes could be modelled
MTLLGST01000009:12,526–12,729AMTLA10fewer than 2 genes could be modelled
MTLLGST01000009:132,859–132,966AMTLA20fewer than 2 genes could be modelled
MTLLGST01000003:171,592–174,558AMTLA1, MTLA20fewer than 2 genes could be modelled
MTLLGST01000003:289,968–290,207alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000057:119,640–119,879AMTLA20fewer than 2 genes could be modelled
MTLLGST01000004:134,181–134,342AMTLA20fewer than 2 genes could be modelled
MTLLGST01000075:13,412–13,597AMTLA20fewer than 2 genes could be modelled
MTLLGST01000041:48,569–48,718alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000041:180,054–180,224alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000041:293,413–293,592AMTLA10fewer than 2 genes could be modelled
MTLLGST01000073:4,350–4,586AMTLA10fewer than 2 genes could be modelled
MTLLGST01000047:6,771–6,911AMTLA20fewer than 2 genes could be modelled
MTLLGST01000047:110,287–110,559AMTLA20fewer than 2 genes could be modelled
MTLLGST01000006:87,002–87,202alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000008:329,779–352,854AMTLA2, MTLalpha1, MTLalpha20fewer than 2 genes could be modelled
MTLLGST01000008:480,359–480,463alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000034:18,202–18,327AMTLA10fewer than 2 genes could be modelled
MTLLGST01000034:120,570–120,734alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000034:148,256–148,399AMTLA20fewer than 2 genes could be modelled
MTLLGST01000013:92,733–92,945alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000026:18,654–39,215AMTLA1, MTLalpha10fewer than 2 genes could be modelled
MTLLGST01000035:116,891–117,001AMTLA10fewer than 2 genes could be modelled
MTLLGST01000063:7,758–7,889alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000040:353,343–353,459AMTLA10fewer than 2 genes could be modelled
MTLLGST01000040:412,040–412,210AMTLA20fewer than 2 genes could be modelled
MTLLGST01000017:111,386–111,508AMTLA20fewer than 2 genes could be modelled
MTLLGST01000017:187,311–187,520AMTLA20fewer than 2 genes could be modelled
MTLLGST01000037:81,438–81,530AMTLA20fewer than 2 genes could be modelled
MTLLGST01000021:2,884–3,015AMTLA10fewer than 2 genes could be modelled
MTLLGST01000021:123,580–123,819AMTLA20fewer than 2 genes could be modelled
MTLLGST01000029:18,562–18,678alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000029:97,820–97,933AMTLA10fewer than 2 genes could be modelled
MTLLGST01000066:52,162–52,431AMTLA10fewer than 2 genes could be modelled
MTLLGST01000027:167,610–167,708alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000027:209,029–209,127alphaMTLalpha10fewer than 2 genes could be modelled
MTLLGST01000064:37,354–37,536AMTLA20fewer than 2 genes could be modelled
MTLLGST01000019:164,798–166,057undeterminedOBP11too few of the family's genes found

Provenance

Genome file
Cauris6684.genome.fasta
Assembly
99 contigs · 12.5 Mb · N50 267.0 kb
Genome SHA-256
b0a84b5bac4d564273b6d17ec7f3bec439414a31bef176eb5dadeebd69e442e5
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': 27319, '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': 12, 'genetic_code_from': 'family taxid 27319', 'routed_by': 'family taxid 27319 (lineage)'}, genetic_code=12, 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, supported_min_bitscore=33.0
Run started
2026-11-07T02:19:03Z
Run time
31 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