MATPredict · mating-type report

FmangiferaeMRC7560

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 01:54 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 FCQH01000004MAT1-2 locus: genes from left to right on FCQH01000004, 363,184 to 376,528: SLA2 (conserved flank, plus 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).365 kb370 kb375 kb← 362.5 kb more to contig endcalled locusSLA2: conserved flank, 363,184–366,764 (+), identity 81.6%, search hit onlySLA2MAT1-1-3: core MAT gene, 371,702–372,476 (+), identity 40.3%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 371,702–372,476 (+), identity 89.7%, search hit onlyMAT1-2-1APN2: conserved flank, 373,242–375,255 (-), identity 86.4%, search hit onlyAPN2COX13: conserved flank, 375,767–376,528 (+), identity 70.7%, search hit onlyCOX13
Gene order on FCQH01000004. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on FCQH01000004, 362,517 to 377,195FMAN_08692 363,184-366,764 (+): Probable cytoskeleton assembly control protein SLA2 [Source:UniProtKB/TrEMBL;Acc:A0A1L7T4J9]FMAN_08692FMAN_08693 369,341-370,103 (-): unspecified productFMAN_08693FMAN_08694 371,702-372,476 (+): HMG box domain-containing protein [Source:UniProtKB/TrEMBL;Acc:G3G2G4]FMAN_08694FMAN_08695 373,242-375,255 (-): Endo/exonuclease/phosphatase domain-containing protein [Source:UniProtKB/TrEMBL;Acc:A0A1L7T600]FMAN_08695FMAN_08696 375,767-376,528 (+): Related to cytochrome-c oxidase chain VIa [Source:UniProtKB/TrEMBL;Acc:A0A1L7T4M0]FMAN_08696
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
FCQH01000004:363,184–376,528 · 13.3 kb
Own genes
FCQH01000004:363,184–376,528 · 13.3 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
363.2 kb
Region (samtools)
FCQH01000004:363184-376528
Idiomorph scores
  • MAT1-2 398.0

Margin over the set-aside MAT1-1-3 hit: 49.4 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
MAT1-2-189.7MAT1-1-340.3100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome81.6cov 100.0%< 1e-1801,371 bits363,184–366,764 +–107463_unknown-1_MAT_MAT1-2FMAN_08692
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome40.3cov 40.0%9.4e-1460 bits371,702–372,476 +–230073_uamh-1363_MAT_MAT1-1FMAN_08694
MAT1-2-1core MAThit onlyDIAMOND, proteome89.7cov 100.0%1.2e-145398 bits371,702–372,476 +–5127_mo45_MAT_MAT1-2FMAN_08694
APN2conserved flankhit onlyDIAMOND, proteome86.4cov 36.7%6.0e-218610 bits373,242–375,255 -–2903220_liq80xsp_MAT_combinedFMAN_08695
COX13conserved flankhit onlyDIAMOND, proteome70.7cov 89.2%1.6e-63183 bits375,767–376,528 +–578113_sxlc146_MAT_MAT1-2FMAN_08696

Withheld candidate loci 3

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 (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATFCQH01000001:44,923–58,414MAT1-2MAT1-2-1, MAT1-1-41too few of the family's genes found
MATFCQH01000002:1,460,938–1,461,709MAT1-1MAT1-1-11too few of the family's genes found
MATFCQH01000002:2,657,886–2,660,063MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
FmangiferaeMRC7560.genome.fasta
Assembly
254 contigs · 46.3 Mb · N50 2.5 Mb
Genome SHA-256
8a25c439a2f40bdc5b98ba19b790491735ea02a0e032540f452eb514bd0ea4c7
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': 110618, '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 110618', 'routed_by': 'family taxid 110618 (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
2026-11-07T01:53:33Z
Run time
81 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