MATPredict · mating-type report

NglabratusDSY562

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 02:42 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 CM008082MATalpha locus: genes from left to right on CM008082, 13,469 to 14,989: 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← 13.2 kb more to contig endcalled locusMATALPHA1: core MAT gene, 13,469–14,023 (-), identity 44.9%, search hit onlyMATALPHA1MATA2: core MAT gene, 14,357–14,989 (+), identity 52.6%, search hit onlyMATA2MATALPHA2: core MAT gene, 14,357–14,989 (+), identity 49.3%, search hit onlyMATALPHA2
Gene order on CM008082. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on CM008082, 13,169 to 15,289B1J91_B00220g 13,272-13,502 (+): EMG1/NEP1 methyltransferase | domain-containing proteinB1J91_B00220gB1J91_B00242g 13,469-14,023 (-): Mating-type protein MAT alpha 1 HMG-box | domain-containing proteinB1J91_B00242gB1J91_B00264g 14,357-14,989 (+): Homeodomain | domain-containing proteinB1J91_B00264g MTL3alpha2
FungiDB release 71 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
CM008082:13,469–14,989 · 1.5 kb
Cross-lineage class
MAT1-1
Own genes
CM008082:13,469–14,989 · 1.5 kb
Locus
Genes of both idiomorphs at one locus.
Genes modelled
2 of 3 gene hits
Nearest contig end
13.5 kb
Region (samtools)
CM008082:13469-14989
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 bits13,469–14,023 -–4932_s288c_MATsc_MATalphaB1J91_B00220g (opposite strand)
B1J91_B00242g
MATA2core MAThit onlyDIAMOND, proteome52.6cov 75.6%3.6e-2996 bits14,357–14,989 +–4932_s288c_MATsc_HMRaB1J91_B00264g MTL3alpha2
MATALPHA2core MAThit onlyDIAMOND, proteome49.3cov 30.5%7.4e-39123 bits14,357–14,989 +–28985_nrrl-y-1140_MATsc_HMLalphaB1J91_B00264g MTL3alpha2
MATALPHA2expected, not found–
MATA1expected, not found–
cha1not searchable: no reference protein in the database–

Withheld candidate loci 39

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

Show the 39 withheld loci

Withheld loci (39)

familylocationidiomorph genesmodelledreason
MATscCM008082:115,651–116,886MATaMATALPHA1, MATA1, MATA21fewer than 2 genes could be modelled
MATscCM008082:440,313–440,432MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008090:35,298–35,471MATaMATA10fewer than 2 genes could be modelled
MATscCM008090:1,076,382–1,076,477MATaMATA10fewer than 2 genes could be modelled
MATscCM008091:264,121–264,213MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008091:380,829–380,936undeterminedMATA20fewer than 2 genes could be modelled
MATscCM008091:688,622–688,837MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008091:1,037,902–1,038,108undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008091:1,248,956–1,249,132MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008085:45,975–47,201MATaMATALPHA1, MATA1, MATA21fewer than 2 genes could be modelled
MATscCM008083:253,002–253,259undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008088:284,865–285,080undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008088:315,922–316,131MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008088:571,890–572,081MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008087:73,028–73,219undeterminedMATALPHA2, MATA20fewer than 2 genes could be modelled
MATscCM008087:607,420–607,521undeterminedMATA20fewer than 2 genes could be modelled
MATscCM008087:717,114–717,287MATaMATA10fewer than 2 genes could be modelled
MATscCM008087:784,340–784,513undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008089:36,228–36,332MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008089:131,844–132,116MATaMATA10fewer than 2 genes could be modelled
MATscCM008089:206,112–206,432undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008089:512,475–512,681MATaMATA10fewer than 2 genes could be modelled
MATscCM008093:580,241–585,929MATalphaMATALPHA1, MATALPHA20fewer than 2 genes could be modelled
MATscCM008093:667,174–667,296MATaMATA10fewer than 2 genes could be modelled
MATscCM008093:864,962–865,066MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008093:1,411,354–1,411,512undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008084:218,509–218,646undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008084:556,736–556,969undeterminedMATA20fewer than 2 genes could be modelled
MATscCM008084:583,990–584,133undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008086:136,068–136,319MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008086:283,747–283,884undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008086:521,190–521,312MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008086:571,406–571,567MATaMATA10fewer than 2 genes could be modelled
MATscCM008086:1,246,871–1,247,059undeterminedMATA20fewer than 2 genes could be modelled
MATscCM008086:1,481,014–1,481,229MATalphaMATALPHA10fewer than 2 genes could be modelled
MATscCM008086:1,554,680–1,554,943undeterminedMATA20fewer than 2 genes could be modelled
MATscCM008092:30,460–30,564undeterminedMATALPHA20fewer than 2 genes could be modelled
MATscCM008092:147,138–147,332MATaMATA10fewer than 2 genes could be modelled
MATscCM008090:783,121–785,979undeterminedsla21too few of the family's genes found

Provenance

Genome file
NglabratusDSY562.genome.fasta
Assembly
19 contigs · 12.7 Mb · N50 1.2 Mb
Genome SHA-256
b8add6209523249857c8c0a6f559a3db044c5af354494fe14629ca5b2d02e9f9
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
2026-11-07T02:41:56Z
Run time
14 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