MATPredict · mating-type report

CimmitisRS

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 01:51 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 GG704911MAT1-2 locus: genes from left to right on GG704911, 7,370,949 to 7,383,205: SLA2 (conserved flank, plus strand); CIMG_00407 (core MAT gene, minus strand); MAT1-2-4 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, plus strand); MAT1-2-1 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).7,372 kb7,374 kb7,376 kb7,378 kb7,380 kb7,382 kb1,098.5 kb more to contig end →called locusSLA2: conserved flank, 7,370,949–7,374,880 (+), identity 100.0%, search hit onlySLA2CIMG_00407: core MAT gene, 7,376,659–7,377,555 (-), identity 100.0%, search hit onlyCIMG_00407MAT1-2-4: core MAT gene, 7,376,795–7,376,917 (-), identity 34.146%, search hit onlyMAT1-2-4MAT1-1-3: core MAT gene, 7,378,000–7,379,129 (+), identity 25.6%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 7,378,000–7,379,129 (+), identity 100.0%, search hit onlyMAT1-2-1APN2: conserved flank, 7,379,861–7,381,917 (-), identity 100.0%, search hit onlyAPN2COX13: conserved flank, 7,382,537–7,383,205 (+), identity 100.0%, search hit onlyCOX13
Gene order on GG704911. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on GG704911, 7,370,337 to 7,383,818CIMG_00410 7,367,491-7,370,547 (+): mitochondrial morphology maintaining protein MMM1 domain-containing proteinCIMG_00410CIMG_00409 7,370,753-7,375,220 (+): cytoskeleton assembly control proteinCIMG_00409CIMG_00407 7,376,659-7,377,555 (-): hypothetical proteinCIMG_00407CIMG_00406 7,377,854-7,379,544 (+): HMG domain-containing proteinCIMG_00406CIMG_00405 7,379,688-7,382,013 (-): exodeoxyribonuclease III (xth)CIMG_00405CIMG_00404 7,382,483-7,383,483 (+): Cytochrome c oxidase subunit ViaCIMG_00404CIMG_10544 7,383,638-7,385,272 (-): mannosyltransferase, putativeCIMG_10544
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
  • 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
GG704911:7,370,949–7,383,205 · 12.3 kb
Own genes
GG704911:7,370,949–7,383,205 · 12.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 7 gene hits
Nearest contig end
1.1 Mb
Region (samtools)
GG704911:7370949-7383205
Idiomorph scores
  • MAT1-2 664.0

Margin over the set-aside MAT1-1-3 hit: 74.4 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
MAT1-2-1100.0MAT1-1-325.6100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,811 bits7,370,949–7,374,880 +–5501_rs_MAT_MAT1-2CIMG_00409
CIMG_00407core MAThit onlyDIAMOND, proteome100.0cov 100.0%6.3e-195526 bits7,376,659–7,377,555 -–5501_rs_MAT_MAT1-2CIMG_00407
MAT1-2-4core MAThit onlytblastn34.1cov 16.0%8.9e-0736 bits7,376,795–7,376,917 -–746128_af293_MAT_MAT1-2CIMG_00407
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome25.6cov 83.3%7.2e-1565 bits7,378,000–7,379,129 +–230073_uamh-1363_MAT_MAT1-1CIMG_00406
MAT1-2-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%5.7e-247664 bits7,378,000–7,379,129 +–5501_rs_MAT_MAT1-2CIMG_00406
APN2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,217 bits7,379,861–7,381,917 -–5501_rs_MAT_MAT1-2CIMG_00405
COX13conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%2.9e-94261 bits7,382,537–7,383,205 +–5501_rs_MAT_MAT1-2CIMG_00404

Withheld candidate loci 1

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 (1).

Show the 1 withheld locus

Withheld loci (1)

familylocationidiomorph genesmodelledreason
MATGG704911:4,572,595–4,574,704MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CimmitisRS.genome.fasta
Assembly
7 contigs · 29.0 Mb · N50 4.3 Mb
Genome SHA-256
61c86be1ba381eef5d1b954f9f28d4a6d331ca8e401e3363075c83011e9e45b3
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': 33184, '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 33184', 'routed_by': 'family taxid 33184 (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
2026-11-07T01:50:14Z
Run time
51 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