CimmundaCBS83496 – MATPredict report

Result

Mating type

MAT1-2: MAT gene without flanking genes, medium confidence, 21.4 kb on KN847044.1. Gene order: MAT1-2-1 · MAT1-1-3.

Called loci 1

MAT1-2 MAT family · Ascomycota

medium confidence

Gene order on KN847044.1. Scroll sideways to see the whole figure.

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
gene model
tools disagree
alternate model

Location: KN847044.1:1,019,161–1,040,533 · 21.4 kb
Own genes: KN847044.1:1,025,402–1,025,710 · 309 bp · the span runs 21.1 kb beyond these genes
Supported span: KN847044.1:1,025,207–1,026,106 · 900 bp · 20.5 kb of the reported span rests only on hits below 33 bits
Locus: A MAT gene with no flanking gene beside it; not a full locus.
Genes modelled: 2 of 2 gene hits
Nearest contig end: 1.0 Mb
Region (samtools): KN847044.1:1019161-1040533
Detection pass: relaxed

Idiomorph scores

MAT1-2 140.0
MAT1-1 27.3

No other idiomorph scored.

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

Gene evidence

Gene	Role	Model	Identity %	E-value	Position (strand)	Exons	Reference record	FungiDB gene
MAT1-2-1	core MAT	models differexonerateminiprot: 1,025,402–1,026,076, 39.5%	54.4cov 30.5%	9.5e-37140 bits	1,025,402–1,025,710 -	1	199306_silveira_MAT_MAT1-2	none
MAT1-1-3	core MAT	gene modelexonerate	33.3cov 41.7%	9.8e+0027 bits	1,025,450–1,025,674 -	1	230073_uamh-1363_MAT_MAT1-1	none
MAT1-1-1	expected, not found							–
APN2	expected, not found							–
SLA2	expected, not found							–
COX13	expected, not found							–

What was searched

Routing: By taxonomy. The genome's taxonomy falls inside a curated family's scope; only those families were searched.
Families searched: Ascomycota:MAT
Genetic code: 1
Taxonomy: local NCBI taxonomy snapshot 2026-10-01

Withheld candidate loci 34

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 (29); too few of the family's genes found (5).

Show the 34 withheld loci

Withheld loci (34)

family	location	idiomorph	genes	modelled	reason
MAT	KN847044.1:1,672,140–1,693,844	MAT1-2	MAT1-2-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	KN847044.1:2,123,499–2,140,086	MAT1-2	MAT1-2-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	KN847044.1:2,967,235–2,988,868	MAT1-2	MAT1-2-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847044.1:3,674,488–3,681,745	MAT1-1	MAT1-1-1, MAT1-2-4	0	fewer than 2 genes could be modelled
MAT	KN847041.1:1,697,545–1,712,517	MAT1-1	MAT1-2-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	KN847041.1:1,933,062–1,962,467	MAT1-2	MAT1-2-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847041.1:2,532,648–2,551,220	MAT1-2	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847041.1:3,147,483–3,170,413	MAT1-2	MAT1-1-1, MAT1-2-1	1	fewer than 2 genes could be modelled
MAT	KN847041.1:3,512,927–3,528,637	MAT1-1	MAT1-1-1, MAT1-2-7	0	fewer than 2 genes could be modelled
MAT	KN847041.1:3,587,213–3,598,339	MAT1-1	MAT1-1-2, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847041.1:3,686,301–3,709,835	MAT1-1	MAT1-1-3, MAT1-1-4	0	fewer than 2 genes could be modelled
MAT	KN847041.1:4,094,446–4,119,175	MAT1-2	MAT1-2-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	KN847041.1:5,272,329–5,282,924	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847046.1:365,090–384,741	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847046.1:429,186–435,883	MAT1-1	MAT1-1-1, MAT1-2-7	0	fewer than 2 genes could be modelled
MAT	KN847046.1:1,382,863–1,387,931	MAT1-1	MAT1-1-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	KN847046.1:3,119,607–3,128,327	MAT1-2	MAT1-2-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847043.1:906,385–931,619	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847043.1:2,535,740–2,538,575	MAT1-2	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847043.1:5,096,704–5,124,942	MAT1-1	MAT1-1-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	KN847042.1:136,322–145,311	MAT1-1	MAT1-1-1, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	KN847042.1:609,902–629,428	MAT1-1	MAT1-1-1, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	KN847042.1:2,305,576–2,327,695	MAT1-1	MAT1-1-1, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	KN847042.1:3,906,673–3,921,400	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847042.1:5,521,130–5,536,925	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	KN847040.1:864,924–877,242	MAT1-2	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847040.1:2,287,021–2,297,019	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847040.1:3,375,093–3,392,144	undetermined	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847040.1:4,116,925–4,138,809	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	KN847044.1:681,597–683,458	undetermined	APN2	1	too few of the family's genes found
MAT	KN847044.1:1,722,195–1,725,505	undetermined	SLA2	1	too few of the family's genes found
MAT	KN847044.1:2,567,861–2,568,425	undetermined	COX13	1	too few of the family's genes found
MAT	KN847045.1:3,376,946–3,379,802	MAT1-2	MAT1-2-1	1	too few of the family's genes found
MAT	KN847041.1:3,147,483–3,170,413	MAT1-2	MAT1-1-1, MAT1-2-1	1	too few of the family's genes found

Provenance

Genome file: CimmundaCBS83496.genome.fasta
Assembly: 277 contigs · 43.0 Mb · N50 6.0 Mb
Genome SHA-256: 15b657f5bdbe9c08b2692970caebc1312c18958fc4b6674d9062181c33130489
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': 43219, '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 43219', 'routed_by': 'family taxid 43219 (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: 2026-11-07T01:52:03Z
Run time: 85 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

MATPredict reads an assembly; it is not a mating assay. Two idiomorphs in one assembly can come from a homothallic species, a mixed culture or a merged diploid assembly.
Fragmented assemblies can split a locus or lose its flanking genes; an uncalled genome is weak evidence of absence.
Lineages with no curated record are searched with the whole phylum's references; family labels there are less reliable.