MATPredict · mating-type report

CmetapsilosisBP57

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

Ahigh confidence

Called loci 1

A MTL family · Ascomycota

high confidence
Gene order of the A locus on JAEOAQ010000005A locus: genes from left to right on JAEOAQ010000005, 857,755 to 865,403: MTLalpha2 (core MAT gene, minus strand); OBP1 (variable flank, plus strand); PIK1 (variable flank, plus strand); MTLA2 (core MAT gene, plus strand); MTLA1 (core MAT gene, plus strand).858 kb860 kb862 kb864 kb215.0 kb more to contig end →called locusMTLalpha2: core MAT gene, 857,758–858,189 (-), identity 30.065%, search hit onlyMTLalpha2 (lost to MTLA1)OBP1: variable flank, 858,905–860,206 (+), identity 69.0%, search hit onlyOBP1PIK1: variable flank, 860,434–863,274 (+), identity 62.8%, search hit onlyPIK1MTLA2: core MAT gene, 864,079–864,632 (+), identity 41.2%, search hit onlyMTLA2MTLA1: core MAT gene, 864,968–865,403 (+), identity 39.02%, gene modelMTLA1
Gene order on JAEOAQ010000005. Scroll sideways to see the whole figure.
FungiDB release 68 gene models on JAEOAQ010000005, 857,373 to 865,785I9W82_004115 855,950-857,650 (+): hypothetical proteinI9W82_004115I9W82_004116 857,686-858,198 (-): HMLALPHA2I9W82_004116I9W82_004117 858,905-860,206 (+): OSH6I9W82_004117I9W82_004118 860,434-863,274 (+): pik1I9W82_004118I9W82_004119 864,079-864,632 (+): hypothetical proteinI9W82_004119I9W82_004120 865,711-867,858 (-): hypothetical proteinI9W82_004120
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
  • variable flank
  • gene model
  • search hit only
  • MTLalpha2 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
JAEOAQ010000005:857,755–865,403 · 7.6 kb
Cross-lineage class
MAT1-2
Own genes
JAEOAQ010000005:857,758–865,403 · 7.6 kb · the span runs 3 bp beyond these genes
Supported span
JAEOAQ010000005:857,758–865,403 · 7.6 kb · 3 bp of the reported span rests only on hits below 33 bits
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
4 of 5 gene hits
Nearest contig end
215.4 kb
Region (samtools)
JAEOAQ010000005:857755-865403
Idiomorph scores
  • A 74.7

Margin over the set-aside MTLalpha2 hit: 0.9 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
MTLA131.0MTLalpha230.1100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
MTLalpha2core MATother idiomorph, not countedlost to MTLA1, not countedhit onlytblastn30.1cov 75.0%8.9e-1457 bits857,758–858,189 -–42374_d1558_MTL_alphaI9W82_004116
OBP1variable flankhit onlyDIAMOND, proteome69.0cov 98.8%3.5e-212583 bits858,905–860,206 +–5476_sc5314_MTL_AI9W82_004117
PIK1variable flankhit onlyDIAMOND, proteome62.8cov 99.3%< 1e-1801,090 bits860,434–863,274 +–5476_sc5314_MTL_AI9W82_004118
MTLA2core MAThit onlyDIAMOND, proteome41.2cov 55.2%3.9e-2075 bits864,079–864,632 +–5476_sc5314_MTL_AI9W82_004119
MTLA1core MATgene modelexonerate39.0cov 58.6%1.8e-1264 bits864,968–865,403 +25476_sc5314_MTL_Anone

Withheld candidate loci 29

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: fewer than 2 genes could be modelled (27); too few of the family's genes found (2).

Show the 29 withheld loci

Withheld loci (29)

familylocationidiomorph genesmodelledreason
MTLJAEOAQ010000002:194,478–194,567AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000002:1,123,201–1,123,317alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000002:1,489,005–1,489,331AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000002:1,548,689–1,548,946AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000002:1,842,879–1,843,007AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000005:972,130–972,243AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000005:1,004,628–1,004,852AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000007:143,708–143,845AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000007:354,687–354,791alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000007:385,912–386,028AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000007:1,003,071–1,009,119AMTLA1, MTLalpha1, OBP11fewer than 2 genes could be modelled
MTLJAEOAQ010000007:1,202,505–1,202,663alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000007:1,404,366–1,404,521alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:63,867–64,037alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:254,463–254,588AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000001:290,205–305,369alphaMTLA2, MTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:1,221,102–1,221,209alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:1,587,599–1,587,715alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:1,797,979–1,798,110alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000001:2,448,104–2,448,202alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000004:152,422–152,592AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000004:293,904–294,026AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000004:545,446–545,601AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000006:56,103–56,297AMTLA10fewer than 2 genes could be modelled
MTLJAEOAQ010000003:755,684–755,806alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000003:1,238,222–1,238,320alphaMTLalpha10fewer than 2 genes could be modelled
MTLJAEOAQ010000009:85,923–86,117AMTLA20fewer than 2 genes could be modelled
MTLJAEOAQ010000002:2,047,474–2,053,224undeterminedPIK11too few of the family's genes found
MTLJAEOAQ010000007:1,542,051–1,545,119undeterminedPIK11too few of the family's genes found

Provenance

Genome file
CmetapsilosisBP57.genome.fasta
Assembly
9 contigs · 13.1 Mb · N50 2.1 Mb
Genome SHA-256
0f7ad6bf9a5979e9069594467b366fee3389352f67a6f056c7969e8230575be1
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': 766764, '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': 12, 'genetic_code_from': 'family taxid 766764', 'routed_by': 'family taxid 766764 (lineage)'}, genetic_code=12, 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, supported_min_bitscore=33.0
Run started
2026-11-07T01:53:52Z
Run time
21 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