MATPredict · mating-type report

NglabratusBG3993

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 02:05 UTC by MATPredict 0.8.1

Result

Mating type

MATalphamedium confidence

Called loci 1

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP053487MATalpha locus: genes from left to right on CP053487, 13,056 to 14,577: MATALPHA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand); MATALPHA2 (core MAT gene, plus strand).13.0 kb13.5 kb14.0 kb14.5 kb← 12.8 kb more to contig endcalled locusMATALPHA1: core MAT gene, 13,056–13,631 (-), identity 44.9%, search hit onlyMATALPHA1MATA2: core MAT gene, 13,945–14,577 (+), identity 52.6%, search hit onlyMATA2MATALPHA2: core MAT gene, 13,945–14,577 (+), identity 49.3%, search hit onlyMATALPHA2
Gene order on CP053487. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP053487, 12,756 to 14,877GW608_B00055 12,859-13,089 (+): Ribosomal RNA small subunit methyltransferase NEP1 [Source:UniProtKB/TrEMBL;Acc:A0A0W0C632]GW608_B00055GW608_B00077 13,056-13,631 (-): unspecified productGW608_B00077GW608_B00099 13,945-14,577 (+): MTLalpha2GW608_B00099 MTLalpha2
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
  • search hit only
Location
CP053487:13,056–14,577 · 1.5 kb
Cross-lineage class
MAT1-1
Own genes
CP053487:13,056–14,577 · 1.5 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
2 of 3 gene hits
Nearest contig end
13.1 kb
Region (samtools)
CP053487:13056-14577
Idiomorph scores
  • MATalpha 87.4

Margin over the set-aside MATALPHA2 hit: 3.3 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
MATA252.6MATALPHA249.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATALPHA1core MAThit onlyDIAMOND, proteome44.9cov 50.9%1.7e-2587 bits13,056–13,631 -–4932_s288c_MATsc_MATalphaGW608_B00055 (opposite strand)
GW608_B00077
MATA2core MAThit onlyDIAMOND, proteome52.6cov 75.6%3.6e-2996 bits13,945–14,577 +–4932_s288c_MATsc_HMRaGW608_B00099 MTLalpha2
MATALPHA2core MAThit onlyDIAMOND, proteome49.3cov 30.5%7.4e-39123 bits13,945–14,577 +–28985_nrrl-y-1140_MATsc_HMLalphaGW608_B00099 MTLalpha2
MATALPHA2expected, not found–
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 35

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

Show the 35 withheld loci

Withheld loci (35)

familylocationidiomorph genesmodelledreason
MATscCP053487:115,212–116,438MATaMATALPHA1, MATA1, MATA21fewer than 2 genes could be modelled
MATscCP053495:38,429–38,602MATaMATA10fewer than 2 genes could be modelled
MATscCP053495:1,040,627–1,040,761undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053495:1,092,679–1,092,774MATaMATA10fewer than 2 genes could be modelled
MATscCP053496:263,850–263,942MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053496:380,576–380,683undeterminedMATA20fewer than 2 genes could be modelled
MATscCP053496:423,522–423,737MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053496:688,569–688,784MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053496:1,249,063–1,249,239MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053497:123,854–124,069MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053497:307,172–307,474MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053497:336,606–358,338MATalphaMATALPHA1, MATA20fewer than 2 genes could be modelled
MATscCP053497:691,935–692,039undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053497:808,644–808,838MATaMATA10fewer than 2 genes could be modelled
MATscCP053490:46,591–47,817MATaMATALPHA1, MATA1, MATA21fewer than 2 genes could be modelled
MATscCP053488:208,748–208,939undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053493:285,145–285,360undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP053493:316,164–316,373MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053493:576,030–576,221MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053494:39,516–39,620MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053494:135,077–135,349MATaMATA10fewer than 2 genes could be modelled
MATscCP053494:209,263–232,839MATaMATALPHA2, MATA10fewer than 2 genes could be modelled
MATscCP053492:70,622–70,813undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP053492:587,765–587,866undeterminedMATA20fewer than 2 genes could be modelled
MATscCP053492:697,550–697,723MATaMATA10fewer than 2 genes could be modelled
MATscCP053492:764,444–764,617undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053498:578,021–583,722MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MATscCP053498:664,984–665,106MATaMATA10fewer than 2 genes could be modelled
MATscCP053498:863,146–863,250MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053489:223,849–223,986undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053489:568,555–568,788undeterminedMATA20fewer than 2 genes could be modelled
MATscCP053489:595,801–595,944undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP053491:144,474–144,725MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP053491:578,636–578,797MATaMATA10fewer than 2 genes could be modelled
MATscCP053495:799,312–802,170undeterminedsla21too few of the family's genes found

Provenance

Genome file
NglabratusBG3993.genome.fasta
Assembly
13 contigs · 12.7 Mb · N50 1.1 Mb
Genome SHA-256
f6c5afdd4e325dcaca02b2281ec0bb24d162fdf79b498045ddcb49edeefbdf38
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': 4893, '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 4893', 'routed_by': 'family taxid 4893 (direct)'}, 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
2026-11-07T02:04:52Z
Run time
24 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