MATPredict · mating-type report

NglabratusCBS1382020

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 02:06 UTC by MATPredict 0.8.1

Result

Mating-type loci

MATalphamedium confidenceMATalphamedium confidence

Called loci 2

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP048119MATalpha locus: genes from left to right on CP048119, 13,592 to 15,112: MATALPHA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand); MATALPHA2 (core MAT gene, plus strand).13.5 kb14.0 kb14.5 kb15.0 kb← 13.3 kb more to contig endcalled locusMATALPHA1: core MAT gene, 13,592–14,146 (-), identity 44.9%, search hit onlyMATALPHA1MATA2: core MAT gene, 14,480–15,112 (+), identity 52.6%, search hit onlyMATA2MATALPHA2: core MAT gene, 14,480–15,112 (+), identity 49.3%, search hit onlyMATALPHA2
Gene order on CP048119. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP048119, 13,292 to 15,412GVI51_B00055 13,395-13,625 (+): Ribosomal RNA small subunit methyltransferase NEP1 [Source:UniProtKB/TrEMBL;Acc:A0A0W0C632]GVI51_B00055GVI51_B00077 13,592-14,146 (-): unspecified productGVI51_B00077GVI51_B00099 14,480-15,112 (+): MTLalpha2GVI51_B00099
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
CP048119:13,592–15,112 · 1.5 kb
Cross-lineage class
MAT1-1
Own genes
CP048119:13,592–15,112 · 1.5 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
2 of 3 gene hits
Nearest contig end
13.6 kb
Region (samtools)
CP048119:13592-15112
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%1.4e-2587 bits13,592–14,146 -–4932_s288c_MATsc_MATalphaGVI51_B00055 (opposite strand)
GVI51_B00077
MATA2core MAThit onlyDIAMOND, proteome52.6cov 75.6%3.6e-2996 bits14,480–15,112 +–4932_s288c_MATsc_HMRaGVI51_B00099
MATALPHA2core MAThit onlyDIAMOND, proteome49.3cov 30.5%7.4e-39123 bits14,480–15,112 +–28985_nrrl-y-1140_MATsc_HMLalphaGVI51_B00099
MATALPHA2expected, not found–
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

MATalpha MATsc family · Ascomycota

medium confidence
Gene order of the MATalpha locus on CP048119MATalpha locus: genes from left to right on CP048119, 115,841 to 117,289: MATALPHA1 (core MAT gene, minus strand); MATA2 (core MAT gene, plus strand); MATALPHA2 (core MAT gene, plus strand).116.0 kb116.5 kb117.0 kb117.5 kb← 115.5 kb more to contig endcalled locusMATALPHA1: core MAT gene, 115,841–116,272 (-), identity 44.9%, search hit onlyMATALPHA1MATA2: core MAT gene, 116,729–117,289 (+), identity 52.0%, search hit onlyMATA2MATALPHA2: core MAT gene, 116,729–117,289 (+), identity 48.4%, search hit onlyMATALPHA2
Gene order on CP048119. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on CP048119, 115,541 to 117,589GVI51_B01067 115,185-115,874 (+): EMG1GVI51_B01067GVI51_B01089 115,841-116,272 (-): MATalpha1GVI51_B01089GVI51_B01111 116,729-117,289 (+): MATalpha2GVI51_B01111
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
CP048119:115,841–117,289 · 1.4 kb
Cross-lineage class
MAT1-1
Own genes
CP048119:115,841–117,289 · 1.4 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
2 of 3 gene hits
Nearest contig end
115.8 kb
Region (samtools)
CP048119:115841-117289
Idiomorph scores
  • MATalpha 87.4

Margin over the set-aside MATALPHA2 hit: 3.6 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
MATA252.0MATALPHA248.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MATALPHA1core MAThit onlyDIAMOND, proteome44.9cov 50.9%4.0e-2687 bits115,841–116,272 -–4932_s288c_MATsc_MATalphaGVI51_B01067 (opposite strand)
GVI51_B01089
MATA2core MAThit onlyDIAMOND, proteome52.0cov 77.3%9.0e-3097 bits116,729–117,289 +–4932_s288c_MATsc_HMRaGVI51_B01111
MATALPHA2core MAThit onlyDIAMOND, proteome48.4cov 27.8%1.7e-39124 bits116,729–117,289 +–28985_nrrl-y-1140_MATsc_HMLalphaGVI51_B01111
MATALPHA2expected, not found–
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 37

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

Show the 37 withheld loci

Withheld loci (37)

familylocationidiomorph genesmodelledreason
MATscCP048127:38,461–38,634MATaMATA10fewer than 2 genes could be modelled
MATscCP048127:1,034,374–1,034,487undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048127:1,086,403–1,086,498MATaMATA10fewer than 2 genes could be modelled
MATscCP048128:264,912–265,004MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048128:381,645–381,752undeterminedMATA20fewer than 2 genes could be modelled
MATscCP048128:689,559–689,774MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048128:1,038,872–1,039,078undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048128:1,249,908–1,250,084MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048118:341,497–341,736MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048126:115,077–115,292MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048126:327,658–327,759MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048126:533,670–533,942MATaMATA10fewer than 2 genes could be modelled
MATscCP048126:607,790–608,110undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048126:714,499–714,675MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048126:913,984–914,190MATaMATA10fewer than 2 genes could be modelled
MATscCP048122:44,026–45,252MATaMATALPHA1, MATALPHA2, MATA11fewer than 2 genes could be modelled
MATscCP048120:203,122–203,382undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048125:280,983–281,198undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048125:312,036–312,245MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048125:561,776–561,967MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048124:67,570–67,761undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCP048124:585,928–586,029undeterminedMATA20fewer than 2 genes could be modelled
MATscCP048124:702,178–702,351MATaMATA10fewer than 2 genes could be modelled
MATscCP048124:768,996–769,169undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048130:579,959–585,651MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MATscCP048130:666,885–667,007MATaMATA10fewer than 2 genes could be modelled
MATscCP048130:864,958–865,062MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048121:38,120–38,224MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048121:189,185–189,322undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048121:527,823–528,056undeterminedMATA20fewer than 2 genes could be modelled
MATscCP048121:555,061–555,204undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048129:828,211–828,405MATaMATA10fewer than 2 genes could be modelled
MATscCP048129:945,036–945,140undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCP048123:155,896–156,147MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048123:533,993–534,115MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCP048123:584,194–584,355MATaMATA10fewer than 2 genes could be modelled
MATscCP048127:792,997–795,855undeterminedsla21too few of the family's genes found

Provenance

Genome file
NglabratusCBS1382020.genome.fasta
Assembly
13 contigs · 12.7 Mb · N50 1.1 Mb
Genome SHA-256
d6297ed9f5277f5206642810f4b081dcb56f70d8746a52632a7e7298dfb437fc
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
2026-11-07T02:05:45Z
Run time
23 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