MATPredict · mating-type report

TatrovirideJCM9410

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 02:51 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 BCFX01000001MAT1-2 locus: genes from left to right on BCFX01000001, 5,292,623 to 5,305,005: SLA2 (conserved flank, plus strand); COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-2-1 (core MAT gene, minus strand); MAT1-1-3 (core MAT gene, minus strand).5,294 kb5,296 kb5,298 kb5,300 kb5,302 kb5,304 kb1,989.3 kb more to contig end →called locusSLA2: conserved flank, 5,292,638–5,295,983 (+), identity 83.73%, the two modelling tools disagreeSLA2COX13: conserved flank, 5,299,896–5,300,417 (-), identity 69.83%, the two modelling tools disagreeCOX13APN2: conserved flank, 5,301,061–5,302,451 (+), identity 67.7%, the two modelling tools disagreeAPN2MAT1-2-1: core MAT gene, 5,304,334–5,304,818 (-), identity 55.38%, the two modelling tools disagreeMAT1-2-1MAT1-1-3: core MAT gene, 5,304,546–5,304,650 (-), identity 40.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)
Gene order on BCFX01000001. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • tools disagree
  • alternate model
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
BCFX01000001:5,292,623–5,305,005 · 12.4 kb
Own genes
BCFX01000001:5,292,638–5,304,818 · 12.2 kb · the span runs 202 bp beyond these genes
Supported span
BCFX01000001:5,292,623–5,304,896 · 12.3 kb · 109 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
2.0 Mb
Region (samtools)
BCFX01000001:5292623-5305005
Idiomorph scores
  • MAT1-2 81.6

Margin over the set-aside MAT1-1-3 hit: 18.8 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
MAT1-2-152.9MAT1-1-334.1100.0higher identity
MAT1-2-167.5MAT1-1-340.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankmodels differexonerateminiprot: 5,292,626–5,295,986, 83.3%83.7cov 99.7%< 1e-1801,668 bits5,292,638–5,295,983 +4578113_sxlc146_MAT_MAT1-2
COX13conserved flankmodels differexonerateminiprot: 5,299,680–5,300,417, 66.2%69.8cov 88.0%1.1e-40143 bits5,299,896–5,300,417 -227337_vdls-17_MAT_MAT1-2
APN2conserved flankmodels differexonerateminiprot: 5,300,916–5,303,495, 48.5%67.7cov 76.7%< 1e-180577 bits5,301,061–5,302,451 +327337_vdls-17_MAT_MAT1-2
MAT1-2-1core MATmodels differexonerateminiprot: 5,304,280–5,304,818, 46.7%55.4cov 59.2%1.6e-2782 bits5,304,334–5,304,818 -35127_mo45_MAT_MAT1-2
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlytblastn40.0cov 19.0%1.0e-0433 bits5,304,546–5,304,650 -–230073_uamh-1363_MAT_MAT1-1

Withheld candidate loci 17

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 (17).

Show the 17 withheld loci

Withheld loci (17)

familylocationidiomorph genesmodelledreason
MATBCFX01000001:1,093,566–1,158,428MAT1-2MAT1-1-1, MAT1-2-1, SLA2, MAT1-2-101fewer than 2 genes could be modelled
MATBCFX01000002:2,649,479–2,664,574MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATBCFX01000002:3,276,665–3,289,972MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATBCFX01000002:4,740,629–4,766,834MAT1-2MAT1-2-1, APN2, SLA20fewer than 2 genes could be modelled
MATBCFX01000007:1,405,455–1,407,585MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATBCFX01000004:1,866,390–1,872,567MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATBCFX01000004:1,927,534–1,932,613MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATBCFX01000003:1,383,714–1,415,542undeterminedMAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled
MATBCFX01000003:1,846,154–1,852,743MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATBCFX01000003:2,150,421–2,173,494MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATBCFX01000003:2,628,685–2,635,300MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATBCFX01000003:4,231,782–4,238,854MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATBCFX01000009:955,779–990,463MAT1-1MAT1-1-1, MAT1-2-1, APN20fewer than 2 genes could be modelled
MATBCFX01000006:634,443–651,728MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATBCFX01000006:933,602–934,844MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATBCFX01000006:1,245,787–1,268,217MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATBCFX01000006:2,207,420–2,217,023MAT1-1MAT1-1-1, COX13, MAT1-1-20fewer than 2 genes could be modelled

Provenance

Genome file
TatrovirideJCM9410.genome.fasta
Assembly
23 contigs · 37.3 Mb · N50 5.6 Mb
Genome SHA-256
5e47ed4609960162d45d1dc9f41bccc2e54147cb819e12b1d82dbfa446a93d89
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': 5129, '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 5129', 'routed_by': 'family taxid 5129 (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
2026-11-07T02:50:07Z
Run time
104 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