MATPredict · mating-type report

CimmitisRMSCC3703

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 01:50 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 DS268188.1MAT1-1 locus: genes from left to right on DS268188.1, 106,059 to 118,643: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand); MAT1-1-4 (core MAT gene, minus strand); APN2 (conserved flank, minus strand); COX13 (conserved flank, plus strand).106 kb108 kb110 kb112 kb114 kb116 kb118 kbcontig endcalled locusSLA2: conserved flank, 106,059–109,993 (+), identity 99.62%, gene modelSLA2MAT1-1-1: core MAT gene, 112,100–113,319 (-), identity 99.74%, gene modelMAT1-1-1MAT1-1-4: core MAT gene, 113,920–118,047 (-), identity 78.89%, the two modelling tools disagreeMAT1-1-4APN2: conserved flank, 115,768–117,514 (-), identity 99.82%, gene modelAPN2COX13: conserved flank, 118,137–118,643 (+), identity 93.75%, the two modelling tools disagreeCOX13
Gene order on DS268188.1. Scroll sideways to see the whole figure.
  • core MAT gene
  • conserved flank
  • gene model
  • tools disagree
  • alternate model
Location
DS268188.1:106,059–118,643 · 12.6 kb
Own genes
DS268188.1:106,059–118,643 · 12.6 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
5 of 5 gene hits
Nearest contig end
19 bp
Region (samtools)
DS268188.1:106059-118643
Idiomorph scores
  • MAT1-1 597.0

No other idiomorph scored.

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

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference record
SLA2conserved flankgene modelexonerate2 frameshiftsdefective gene model99.6cov 100.0%< 1e-180909 bits106,059–109,993 +125501_rs_MAT_MAT1-2
MAT1-1-1core MATgene modelexonerate99.7cov 100.0%< 1e-180597 bits112,100–113,319 -2199306_rmscc1040_MAT_MAT1-1
MAT1-1-4core MATmodels differexonerateminiprot: 113,917–114,976, 41.4%1 internal stopdefective gene model78.9cov 38.2%3.0e-1060 bits113,920–118,047 -5199306_rmscc1040_MAT_MAT1-1
APN2conserved flankgene modelexonerate5 frameshiftsdefective gene model99.8cov 90.8%< 1e-180808 bits115,768–117,514 -3199306_rmscc1040_MAT_MAT1-1
COX13conserved flankmodels differexonerateminiprot: 118,137–118,613, 95.9%1 internal stopdefective gene model93.8cov 97.0%8.6e-68221 bits118,137–118,643 +35501_h538-4_MAT_MAT1-1

Withheld candidate loci 14

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 (14).

Show the 14 withheld loci

Withheld loci (14)

familylocationidiomorph genesmodelledreason
MATDS268124.1:331,416–355,062MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS268131.1:38,535–46,243MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS268131.1:80,106–96,431MAT1-1MAT1-1-1, COX130fewer than 2 genes could be modelled
MATDS268131.1:268,430–286,213MAT1-1MAT1-1-1, SLA20fewer than 2 genes could be modelled
MATDS268213.1:3,079–4,707MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS268224.1:37,244–56,083MAT1-2MAT1-2-1, APN20fewer than 2 genes could be modelled
MATDS268231.1:34,380–46,642MAT1-2MAT1-1-1, MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS268156.1:23,837–69,891MAT1-2MAT1-2-1, APN2, SLA20fewer than 2 genes could be modelled
MATDS268125.1:355,729–375,309MAT1-2MAT1-2-1, SLA20fewer than 2 genes could be modelled
MATDS268140.1:167,302–169,206MAT1-2MAT1-2-1, COX130fewer than 2 genes could be modelled
MATDS268148.1:128,873–171,455MAT1-1MAT1-1-1, APN2, MAT1-1-30fewer than 2 genes could be modelled
MATDS268120.1:455,409–489,360MAT1-1MAT1-1-1, APN2, COX13, MAT1-1-20fewer than 2 genes could be modelled
MATDS268170.1:96,322–103,676MAT1-1MAT1-1-1, APN20fewer than 2 genes could be modelled
MATDS268243.1:14,636–44,708MAT1-1MAT1-1-1, APN2, MAT1-1-30fewer than 2 genes could be modelled

Provenance

Genome file
CimmitisRMSCC3703.genome.fasta
Assembly
289 contigs · 27.7 Mb · N50 233.0 kb
Genome SHA-256
6648c7b2dbc46cfe40b951df20934fc8cc568e741864bb791a1e6166c3252aff
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': 33184, 'routing_taxid_rank': 'family', 'flags': ['high_N'], '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 33184', 'routed_by': 'family taxid 33184 (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
2026-11-07T01:49:11Z
Run time
61 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