Cclavatayc1106 – 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.

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

Families searched but not called

family	reason	best % of genes found	genes found
Ascomycota:MAT	best cluster carried 1 modelled gene(s), below the 2 required to report a locus; only 1 of its genes could be modelled	40.0	MAT1-1-1, MAT1-1-2

Withheld candidate loci 28

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 (24); too few of the family's genes found (4).

Show the 28 withheld loci

Withheld loci (28)

family	location	idiomorph	genes	modelled	reason
MAT	CP089279:1,046,665–1,068,781	MAT1-2	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	CP089279:1,911,350–1,930,634	MAT1-1	MAT1-1-1, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	CP089279:1,991,810–2,005,851	MAT1-1	MAT1-1-1, MAT1-2-4	0	fewer than 2 genes could be modelled
MAT	CP089281:1,432,139–1,433,277	MAT1-1	MAT1-1-1, MAT1-1-2	1	fewer than 2 genes could be modelled
MAT	CP089281:1,856,530–1,862,656	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	CP089274:561,113–573,795	MAT1-2	MAT1-2-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	CP089274:659,453–660,789	MAT1-1	MAT1-1-1, MAT1-2-4	0	fewer than 2 genes could be modelled
MAT	CP089274:1,274,042–1,291,307	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	CP089274:2,720,869–2,737,721	MAT1-2	MAT1-2-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	CP089274:3,369,035–3,374,551	MAT1-1	MAT1-1-1, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	CP089274:3,501,016–3,514,826	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	CP089275:341,968–378,621	MAT1-2	MAT1-2-1, MAT1-1-2, MAT1-1-5	0	fewer than 2 genes could be modelled
MAT	CP089275:2,262,634–2,276,728	MAT1-1	MAT1-1-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	CP089277:529,009–538,722	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	CP089277:1,698,549–1,705,053	MAT1-1	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	CP089277:1,933,773–1,953,664	MAT1-1	MAT1-1-1, MAT1-2-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	CP089277:2,353,159–2,358,320	MAT1-1	MAT1-1-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	CP089277:4,282,967–4,327,309	MAT1-2	MAT1-2-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	CP089278:739,238–742,701	MAT1-1	MAT1-1-1, MAT1-1-4	0	fewer than 2 genes could be modelled
MAT	CP089278:1,544,484–1,546,275	MAT1-2	MAT1-1-1, MAT1-2-1	0	fewer than 2 genes could be modelled
MAT	CP089278:1,697,935–1,702,161	MAT1-2	MAT1-1-3, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	CP089276:1,184,420–1,199,358	MAT1-1	MAT1-1-1, MAT1-1-3	0	fewer than 2 genes could be modelled
MAT	CP089276:2,940,741–2,962,171	MAT1-2	MAT1-2-1, MAT1-1-2	0	fewer than 2 genes could be modelled
MAT	CP089276:4,136,657–4,146,774	MAT1-1	MAT1-1-1, MAT1-2-10	0	fewer than 2 genes could be modelled
MAT	CP089279:1,673,746–1,679,051	MAT1-2	MAT1-2-1	1	too few of the family's genes found
MAT	CP089281:1,062,958–1,068,593	undetermined	APN2, COX13	2	too few of the family's genes found
MAT	CP089281:1,432,139–1,433,277	MAT1-1	MAT1-1-1, MAT1-1-2	1	too few of the family's genes found
MAT	CP089281:1,784,150–1,787,632	undetermined	SLA2	1	too few of the family's genes found

Provenance

Genome file: Cclavatayc1106.genome.fasta
Assembly: 8 contigs · 32.4 Mb · N50 4.7 Mb
Genome SHA-256: c05d2154e3b0e8e228f568160134a922c8ebc71f438ebc79982b6e0689b33b3f
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': 28556, 'routing_taxid_rank': 'family', 'flags': ['identical_to_reference'], '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 28556', 'routed_by': 'family taxid 28556 (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: 2026-11-07T01:51:30Z
Run time: 65 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.