MATPredict · mating-type report

ChigginsianumIMI349063

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

MAT1-2high confidence

Called loci 1

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on LTAN01000007MAT1-2 locus: genes from left to right on LTAN01000007, 829,775 to 846,570: SLA2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, plus strand); MAT1-1-3 (core MAT gene, plus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).830 kb835 kb840 kb845 kb← 828.9 kb more to contig endcalled locusSLA2: conserved flank, 829,775–833,242 (+), identity 85.2%, search hit onlySLA2MAT1-2-1: core MAT gene, 841,428–842,285 (+), identity 50.0%, search hit onlyMAT1-2-1MAT1-1-3: core MAT gene, 841,902–842,186 (+), identity 28.421%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)APN2: conserved flank, 842,569–844,574 (-), identity 81.8%, search hit onlyAPN2COX13: conserved flank, 845,703–846,570 (+), identity 70.8%, search hit onlyCOX13
Gene order on LTAN01000007. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on LTAN01000007, 828,935 to 847,409CH63R_09968 829,775-833,242 (+): SLA2 proteinCH63R_09968CH63R_09969 837,966-839,326 (-): unspecified productCH63R_09969CH63R_09970 841,428-842,285 (+): HMG box proteinCH63R_09970CH63R_09971 842,569-844,574 (-): DNA lyaseCH63R_09971CH63R_09972 845,703-846,570 (+): Cytochrome c oxidase subunit VIaCH63R_09972CH63R_09973 846,870-849,356 (-): Anaphase-promoting complex proteinCH63R_09973
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
LTAN01000007:829,775–846,570 · 16.8 kb
Own genes
LTAN01000007:829,775–846,570 · 16.8 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
829.8 kb
Region (samtools)
LTAN01000007:829775-846570
Idiomorph scores
  • MAT1-2 148.0

Margin over the set-aside MAT1-1-3 hit: 21.6 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
MAT1-2-150.0MAT1-1-328.4100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome85.2cov 100.0%< 1e-1801,499 bits829,775–833,242 +–27337_vdls-17_MAT_MAT1-2CH63R_09968
MAT1-2-1core MAThit onlyDIAMOND, proteome50.0cov 18.6%1.3e-46148 bits841,428–842,285 +–1873960_unknown-2_MAT_MAT1-2CH63R_09970
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn28.4cov 43.0%9.3e-0543 bits841,902–842,186 +–230073_uamh-1363_MAT_MAT1-1CH63R_09970
APN2conserved flankhit onlyDIAMOND, proteome81.8cov 36.7%7.7e-215601 bits842,569–844,574 -–2903220_liq80xsp_MAT_combinedCH63R_09971
COX13conserved flankhit onlyDIAMOND, proteome70.8cov 72.5%4.6e-63182 bits845,703–846,570 +–5158_cbs114723_MAT_unswitchedCH63R_09972

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
MATCM004461:2,989,710–2,991,382MAT1-2MAT1-2-11too few of the family's genes found
MATCM004462:2,311,365–2,313,574MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
ChigginsianumIMI349063.genome.fasta
Assembly
25 contigs · 50.7 Mb · N50 5.2 Mb
Genome SHA-256
3fd01b7a68f12843fe6acb99a425f7a8011c1fdc51ce2e4e84d33dab85a7793c
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': 681950, 'routing_taxid_rank': 'family', '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': 'family taxid 681950', 'routed_by': 'family taxid 681950 (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
2026-11-07T02:04:23Z
Run time
111 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