MATPredict · mating-type report

CmilitarisCM01

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 02:19 UTC by MATPredict 0.8.1

Result

Mating type

MAT1-1high confidence

Called loci 1

MAT1-1 MAT family · Ascomycota

high confidence
Gene order of the MAT1-1 locus on JH126403MAT1-1 locus: genes from left to right on JH126403, 408,101 to 424,848: SLA2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-2 (core MAT gene, minus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).410 kb415 kb420 kb425 kb← 407.3 kb more to contig endcalled locusSLA2: conserved flank, 408,101–411,477 (+), identity 79.8%, search hit onlySLA2MAT1-2-1: core MAT gene, 414,110–414,247 (+), identity 30.435%, search hit onlyMAT1-2-1MAT1-1-1: core MAT gene, 416,720–418,199 (-), identity 49.6%, search hit onlyMAT1-1-1MAT1-1-2: core MAT gene, 418,978–420,043 (-), identity 29.1%, search hit onlyMAT1-1-2APN2: conserved flank, 421,423–423,635 (-), identity 88.6%, search hit onlyAPN2COX13: conserved flank, 424,086–424,848 (+), identity 66.9%, search hit onlyCOX13
Gene order on JH126403. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on JH126403, 407,263 to 425,685CCM_06520 400,946-407,328 (+): ankyrin 2,3/unc44, putativeCCM_06520CCM_06521 408,101-411,477 (+): cytoskeleton assembly control protein Sla2CCM_06521CCM_06522 414,324-416,443 (+): unspecified productCCM_06522CCM_06523 416,720-418,199 (-): mating-type protein MAT 1-1-1CCM_06523CCM_09679 418,978-420,043 (-): mating-type protein MAT 1-1-2CCM_09679CCM_06524 421,423-423,635 (-): DNA lyaseCCM_06524CCM_06525 424,086-424,848 (+): Cytochrome c oxidase, subunit VIaCCM_06525CCM_06526 425,473-427,932 (+): anaphase-promoting complex subunit Apc5, putativeCCM_06526
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
  • MAT1-2-1 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
JH126403:408,101–424,848 · 16.7 kb
Own genes
JH126403:408,101–424,848 · 16.7 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 6 gene hits
Nearest contig end
408.1 kb
Region (samtools)
JH126403:408101-424848
Idiomorph scores
  • MAT1-1 141.0
  • MAT1-2 29.3

Margin over the next idiomorph: 111.7

Score: bitscore of the best core-gene hit for each idiomorph.

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome79.8cov 81.6%< 1e-1801,397 bits408,101–411,477 +–1301501_voucher-215_MAT_MAT1-1CCM_06521
MAT1-2-1core MATother idiomorph, not countedhit onlytblastn30.4cov 13.0%5.6e+0029 bits414,110–414,247 +–28548_06cwm-g22_MAT_combinednone
MAT1-1-1core MAThit onlyDIAMOND, proteome49.6cov 40.9%2.2e-40141 bits416,720–418,199 -–5518_3639_MAT_combinedCCM_06523
MAT1-1-2core MAThit onlyDIAMOND, proteome29.1cov 74.9%1.1e-31116 bits418,978–420,043 -–5518_3639_MAT_combinedCCM_09679
APN2conserved flankhit onlyDIAMOND, proteome88.6cov 36.7%3.3e-208588 bits421,423–423,635 -–2903220_liq80xsp_MAT_combinedCCM_06524
COX13conserved flankhit onlyDIAMOND, proteome66.9cov 100.0%4.9e-63182 bits424,086–424,848 +–27337_vdls-17_MAT_MAT1-2CCM_06525

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
MATJH126401:3,059,909–3,061,994MAT1-2MAT1-2-11too few of the family's genes found
MATJH126403:956,132–957,525MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
CmilitarisCM01.genome.fasta
Assembly
32 contigs · 32.3 Mb · N50 4.6 Mb
Genome SHA-256
272d70a595f7f5f7b4fd845e9532c35f3f4028fa35fee3b5b0f582a922da734f
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': 'genus', 'routing_taxid': 474943, '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 474943', 'routed_by': 'family taxid 474943 (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
2026-11-07T02:18:08Z
Run time
66 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