MATPredict · mating-type report

CspCBS132003

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 02:16 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on QRBJ01000036MAT1-2 locus: genes from left to right on QRBJ01000036, 202,125 to 213,644: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand); SLA2 (conserved flank, plus strand).202 kb204 kb206 kb208 kb210 kb212 kb214 kb34.2 kb more to contig end →called locusCOX13: conserved flank, 202,125–202,659 (-), identity 76.9%, search hit onlyCOX13APN2: conserved flank, 202,991–205,071 (+), identity 86.4%, search hit onlyAPN2MAT1-1-3: core MAT gene, 206,437–207,639 (-), identity 30.4%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 206,437–207,639 (-), identity 61.7%, search hit onlyMAT1-2-1SLA2: conserved flank, 210,409–213,644 (+), identity 80.9%, search hit onlySLA2
Gene order on QRBJ01000036. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on QRBJ01000036, 201,550 to 214,219DV737_g3838 202,125-202,659 (-): Cytochrome c oxidase subunit VIa | domain-containing proteinDV737_g3838DV737_g3839 202,991-205,071 (+): Endonuclease/Exonuclease/phosphatase family | domain-containing proteinDV737_g3839DV737_g3840 206,437-207,639 (-): HMG (high mobility group) box | domain-containing proteinDV737_g3840DV737_g3841 210,409-213,644 (+): ANTH domain | I/LWEQ domain | domain-containing proteinDV737_g3841
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
  • conserved flank
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
QRBJ01000036:202,125–213,644 · 11.5 kb
Own genes
QRBJ01000036:202,125–213,644 · 11.5 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
34.7 kb
Region (samtools)
QRBJ01000036:202125-213644
Idiomorph scores
  • MAT1-2 123.0

Margin over the set-aside MAT1-1-3 hit: 31.3 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
MAT1-2-161.7MAT1-1-330.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome76.9cov 74.3%5.3e-58170 bits202,125–202,659 -–199306_rmscc1040_MAT_MAT1-1DV737_g3838
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%4.2e-208588 bits202,991–205,071 +–2903220_liq80xsp_MAT_combinedDV737_g3839
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome30.4cov 49.7%1.5e-0847 bits206,437–207,639 -–5518_3639_MAT_combinedDV737_g3840
MAT1-2-1core MAThit onlyDIAMOND, proteome61.7cov 26.8%9.9e-35123 bits206,437–207,639 -–1301501_voucher-267_MAT_MAT1-2DV737_g3840
SLA2conserved flankhit onlyDIAMOND, proteome80.9cov 100.0%< 1e-1801,411 bits210,409–213,644 +–1301501_voucher-215_MAT_MAT1-1DV737_g3841

Withheld candidate loci 2

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: too few of the family's genes found (2).

Show the 2 withheld loci

Withheld loci (2)

familylocationidiomorph genesmodelledreason
MATQRBJ01000018:219,076–220,428MAT1-2MAT1-2-11too few of the family's genes found
MATQRBJ01000044:196,382–199,326MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CspCBS132003.genome.fasta
Assembly
118 contigs · 22.9 Mb · N50 312.6 kb
Genome SHA-256
eb7bcea6647ce1be55dd896e4453629f6e0cb0527cddb1b4bad9aec8a51288eb
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': 34395, 'routing_taxid_rank': 'order', 'flags': ['identical_to_reference'], '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': 'order taxid 34395', 'routed_by': 'order taxid 34395 (lineage)'}, 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, scoped_roster=off: BGL1,GAP1 not searched, supported_min_bitscore=33.0
Run started
2026-11-07T02:15:26Z
Run time
63 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