MATPredict · mating-type report

PkudriavzeviiCBS5147

Ascomycota

Run by MATPredict 0.8.1 (v0.8.1, 3a62e6302b) · database 86f18d232e4f · local NCBI taxonomy snapshot 2026-10-01 · rendered 2026-11-07 02:48 UTC by MATPredict 0.8.1

Result

Mating type

MATamedium confidence

Called loci 1

MATa MATsc family · Ascomycota

medium confidence
Gene order of the MATa locus on CP028532MATa locus: genes from left to right on CP028532, 302,754 to 306,262: sla2 (conserved flank, plus strand); MATALPHA2 (core MAT gene, minus strand); MATA1 (core MAT gene, minus strand).303 kb304 kb305 kb306 kb← 302.5 kb more to contig endcalled locussla2: conserved flank, 302,754–303,047 (+), identity 57.14%, the two modelling tools disagreesla2MATALPHA2: core MAT gene, 306,011–306,106 (-), identity 35.294%, search hit onlyMATALPHA2 (lost to MATA1)MATA1: core MAT gene, 306,011–306,151 (-), identity 51.06%, the two modelling tools disagreeMATA1
Gene order on CP028532. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • tools disagree
  • alternate model
  • search hit only
  • The same genes also match: Ascomycota:MTL.
  • MATALPHA2 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
CP028532:302,754–306,262 · 3.5 kb
Cross-lineage class
MAT1-2
Own genes
CP028532:302,754–306,151 · 3.4 kb · the span runs 111 bp beyond these genes
Supported span
CP028532:302,754–306,151 · 3.4 kb · 111 bp of the reported span rests only on hits below 33 bits
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
2 of 3 gene hits
Nearest contig end
302.8 kb
Region (samtools)
CP028532:302754-306262
Idiomorph scores
  • MATa 56.6

Margin over the set-aside MATALPHA2 hit: 25.2 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
MATA160.5MATALPHA235.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
sla2conserved flankmodels differexonerateminiprot: 302,751–305,897, 34.8%57.1cov 14.6%3.8e-80277 bits302,754–303,047 +128985_nrrl-y-1140_MATsc_MATa
MATALPHA2core MATother idiomorph, not countedlost to MATA1, not countedhit onlytblastn35.3cov 15.0%1.0e+0027 bits306,011–306,106 -–28985_nrrl-y-1140_MATsc_HMLalpha
MATA1core MATmodels differexonerateminiprot: 306,002–306,595, 27.6%51.1cov 37.3%1.8e-1057 bits306,011–306,151 -14932_s288c_MATsc_HMRa
MATA2expected, not found
cha1not searchable: no reference protein in the database

Withheld candidate loci 69

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 (69).

Show the 69 withheld loci

Withheld loci (69)

familylocationidiomorph genesmodelledreason
MTLCP028532:66,198–66,365alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028532:124,783–125,061MATaMATA10fewer than 2 genes could be modelled
MTLCP028532:225,656–225,835AMTLA20fewer than 2 genes could be modelled
MTLCP028532:302,754–306,262AMTLA10fewer than 2 genes could be modelled
MTLCP028532:438,467–451,570AMTLA2, MTLalpha10fewer than 2 genes could be modelled
MATscCP028532:747,428–772,218MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028532:955,216–955,329AMTLA10fewer than 2 genes could be modelled
MTLCP028532:1,012,192–1,012,317alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028532:1,071,747–1,071,836AMTLA20fewer than 2 genes could be modelled
MATscCP028532:1,253,073–1,256,734MATaMATA1, sla20fewer than 2 genes could be modelled
MTLCP028532:1,422,780–1,422,911AMTLA20fewer than 2 genes could be modelled
MTLCP028532:1,453,511–1,453,600AMTLA20fewer than 2 genes could be modelled
MATscCP028532:1,576,952–1,591,499MATaMATA10fewer than 2 genes could be modelled
MTLCP028532:1,754,873–1,754,992AMTLA20fewer than 2 genes could be modelled
MTLCP028532:1,879,470–1,888,149alphaMTLalpha1, OBP10fewer than 2 genes could be modelled
MATscCP028532:1,983,286–1,983,396MATaMATA10fewer than 2 genes could be modelled
MATscCP028532:2,084,953–2,090,809MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028532:2,314,502–2,314,663undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028532:2,499,815–2,514,137MATaMATA10fewer than 2 genes could be modelled
MTLCP028532:2,499,815–2,514,137AMTLA1, PAP10fewer than 2 genes could be modelled
MATscCP028531:76,600–116,914MATaMATALPHA1, MATA1, MATA20fewer than 2 genes could be modelled
MTLCP028531:76,600–116,914AMTLA10fewer than 2 genes could be modelled
MTLCP028531:194,395–213,347alphaMTLalpha1, PAP10fewer than 2 genes could be modelled
MATscCP028531:194,395–213,347undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028531:271,230–271,358AMTLA20fewer than 2 genes could be modelled
MATscCP028531:391,498–417,296MATalphaMATALPHA1, sla20fewer than 2 genes could be modelled
MATscCP028531:951,083–965,316undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP028531:1,060,855–1,078,067undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028531:1,432,852–1,449,760alphaMTLalpha1, OBP10fewer than 2 genes could be modelled
MTLCP028531:1,675,712–1,675,801alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028531:1,914,349–1,939,738MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028531:1,966,152–1,966,388MATaMATA10fewer than 2 genes could be modelled
MTLCP028531:1,966,152–1,966,388AMTLA10fewer than 2 genes could be modelled
MTLCP028531:2,256,558–2,256,728AMTLA10fewer than 2 genes could be modelled
MATscCP028531:2,308,695–2,308,811MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028531:2,405,510–2,405,626undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028531:2,580,327–2,580,566MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028531:2,618,406–2,618,702MATaMATA10fewer than 2 genes could be modelled
MATscCP028533:208,730–228,242MATalphaMATALPHA1, MATA20fewer than 2 genes could be modelled
MTLCP028533:307,894–349,008AMTLA1, PIK10fewer than 2 genes could be modelled
MTLCP028533:397,638–397,772alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028533:593,446–593,559AMTLA20fewer than 2 genes could be modelled
MTLCP028533:787,776–789,667AMTLA20fewer than 2 genes could be modelled
MTLCP028533:885,333–888,273AMTLA1, PAP10fewer than 2 genes could be modelled
MTLCP028533:993,334–993,522AMTLA20fewer than 2 genes could be modelled
MTLCP028533:1,020,317–1,023,871AMTLA20fewer than 2 genes could be modelled
MATscCP028533:1,248,457–1,249,170undeterminedMATA20fewer than 2 genes could be modelled
MTLCP028533:1,248,457–1,249,170AMTLA20fewer than 2 genes could be modelled
MTLCP028533:1,408,642–1,408,806AMTLA20fewer than 2 genes could be modelled
MTLCP028533:1,527,854–1,527,964alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028533:1,604,244–1,604,384undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP028533:1,699,909–1,715,811MATaMATA10fewer than 2 genes could be modelled
MTLCP028533:1,699,909–1,715,811AMTLA1, OBP10fewer than 2 genes could be modelled
MATscCP028533:2,419,779–2,430,906MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028534:151,955–152,065alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028534:197,347–199,027undeterminedMATA20fewer than 2 genes could be modelled
MTLCP028534:457,733–457,825alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028534:760,672–771,384MATalphaMATALPHA10fewer than 2 genes could be modelled
MTLCP028534:854,478–854,663AMTLA20fewer than 2 genes could be modelled
MATscCP028534:919,138–926,824MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MTLCP028534:953,984–954,073alphaMTLalpha10fewer than 2 genes could be modelled
MATscCP028534:998,157–1,010,683MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP028534:1,272,729–1,293,170MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MATscCP028534:1,353,124–1,353,222undeterminedMATALPHA20fewer than 2 genes could be modelled
MTLCP028535:223,741–223,842alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028535:525,463–525,567alphaMTLalpha10fewer than 2 genes could be modelled
MTLCP028535:571,304–571,522AMTLA20fewer than 2 genes could be modelled
MTLCP028535:890,229–896,323AMTLA20fewer than 2 genes could be modelled
MTLCP028535:1,201,089–1,201,178AMTLA10fewer than 2 genes could be modelled

Provenance

Genome file
PkudriavzeviiCBS5147.genome.fasta
Assembly
5 contigs · 10.8 Mb · N50 2.7 Mb
Genome SHA-256
1ccf43b6f775770dd80cbca66032f3704a8e446b6638bc9b2f0a66a43ed97b3e
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': 1156497, '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 1156497', 'routed_by': 'family taxid 1156497 (phylum_fallback)'}, 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, supported_min_bitscore=33.0
Run started
2026-11-07T02:48:25Z
Run time
22 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