LcorymbiferaJMRCFSU9682 – MATPredict report

Result

No MAT locus called

No family reached the evidence bar. That is weak evidence that the locus is absent: a fragmented assembly, or a lineage far from every reference, often explains it.

Next: check the withheld candidate loci below against a known locus, or type the strain from its reads.

Assembly gap where the MAT locus is expected: CBTN010000020:269,226–271,071, 1,846 N bases between algA. The assembly never resolved this region, so a missing call here is not evidence of absence.

What was searched

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

Families searched but not called

family	reason	best % of genes found	genes found
Mucoromycota:MAT	best cluster's core gene was not shown to be the MAT gene: classifier score 53.3 bits (model) is below 97.8 or not model-based, and it has 1 roster flank(s) modelled at >= 40% (needs 2)	50.0	tptA, sexP, sexM

Withheld candidate loci 24

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 (16); fewer than 2 genes could be modelled (7); no MAT gene passed the MAT-gene check (1).

Show the 24 withheld loci

Withheld loci (24)

family	location	idiomorph	genes	modelled	reason
MAT	CBTN010000006:49,485–99,141	undetermined	sexP, sexM, rnhA	1	fewer than 2 genes could be modelled
MAT	CBTN010000011:3,383–55,924	undetermined	tptA, sexP, sexM	3	no MAT gene passed the MAT-gene check
MAT	CBTN010000002:648,590–671,022	undetermined	sexP, rnhA	1	fewer than 2 genes could be modelled
MAT	CBTN010000007:467,264–519,152	undetermined	sexM, rnhA	1	fewer than 2 genes could be modelled
MAT	CBTN010000013:237,834–274,109	undetermined	sexP, sexM	1	fewer than 2 genes could be modelled
MAT	CBTN010000039:223,478–262,288	undetermined	sexM, btbA	1	fewer than 2 genes could be modelled
MAT	CBTN010000014:64,395–65,404	undetermined	sexP, sexM	0	fewer than 2 genes could be modelled
MAT	CBTN010000001:55,504–60,663	undetermined	sexP, sexM	0	fewer than 2 genes could be modelled
MAT	CBTN010000002:648,590–671,022	undetermined	sexP, rnhA	1	too few of the family's genes found
MAT	CBTN010000004:62,392–75,719	undetermined	glrA	1	too few of the family's genes found
MAT	CBTN010000006:626,443–627,942	undetermined	algA	1	too few of the family's genes found
MAT	CBTN010000007:467,264–519,152	undetermined	sexM, rnhA	1	too few of the family's genes found
MAT	CBTN010000008:236,387–237,721	undetermined	tptA	1	too few of the family's genes found
MAT	CBTN010000013:237,834–274,109	undetermined	sexP, sexM	1	too few of the family's genes found
MAT	CBTN010000016:155,961–156,988	undetermined	sexM	1	too few of the family's genes found
MAT	CBTN010000020:111,542–116,066	undetermined	rnhA	1	too few of the family's genes found
MAT	CBTN010000020:262,680–264,234	undetermined	algA	1	too few of the family's genes found
MAT	CBTN010000030:318,507–320,429	undetermined	glrA	1	too few of the family's genes found
MAT	CBTN010000039:92,715–97,374	undetermined	btbA	1	too few of the family's genes found
MAT	CBTN010000039:223,478–262,288	undetermined	sexM, btbA	1	too few of the family's genes found
MAT	CBTN010000042:38,944–40,585	undetermined	tptA	1	too few of the family's genes found
MAT	CBTN010000055:164,779–169,811	undetermined	rnhA	1	too few of the family's genes found
MAT	CBTN010000077:20,506–25,094	undetermined	rnhA	1	too few of the family's genes found
MAT	CBTN010000091:88,419–88,961	Minus	sexM	1	too few of the family's genes found

Provenance

Genome file: LcorymbiferaJMRCFSU9682.genome.fasta
Assembly: 209 contigs · 33.5 Mb · N50 367.6 kb
Genome SHA-256: 214c2af01749288264dfc999549fa8b99f3cf3111d42b3e1db7983b3039e7e44
MATPredict: 0.8.1 (v0.8.1, 3a62e6302b)
Database: 86f18d232e4fe95d · 185 records
Taxonomy: local NCBI taxonomy snapshot 2026-10-01
Parameters: phylum=Mucoromycota, phylum_guess={'requested': 'auto', 'status': 'ok', 'usable': True, 'reason': None, 'phylum': 'Mucoromycota', 'phylum_taxid': 1913637, 'deepest_rank': 'species', 'routing_taxid': 499202, '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 Mucoromycota', 'action': 'routed', 'weak_call_accepted': False, 'genetic_code': 1, 'genetic_code_from': 'family taxid 499202', 'routed_by': 'family taxid 499202 (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, supported_min_bitscore=33.0
Run started: 2026-11-07T02:06:19Z
Run time: 41 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.

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.