TciferriiCBS4856 – 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: Whole phylum. No curated family covers this lineage, so every family of the genome's phylum was searched. Family labels are less reliable here.
Families searched: Ascomycota:MATsc, Ascomycota:MTL
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:MATsc	best cluster carried 1 modelled gene(s), below the 2 required to report a locus; only 1 of its genes could be modelled	50.0	MATALPHA1, sla2
Ascomycota:MTL	best cluster carried 1 modelled gene(s), below the 2 required to report a locus; only 1 of its genes could be modelled	100.0	MTLA1

Withheld candidate loci 111

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

Show the 111 withheld loci

Withheld loci (111)

family	location	idiomorph	genes	modelled	reason
MATsc	SWFS01000011:77,342–77,554	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000040:117–272	MATa	MATA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000040:117–272	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000040:33,184–37,438	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000040:33,184–37,438	MATalpha	MATALPHA1, sla2	1	fewer than 2 genes could be modelled
MATsc	SWFS01000432:36,532–38,106	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000432:36,532–38,106	A	MTLA1	1	fewer than 2 genes could be modelled
MATsc	SWFS01000077:120,779–120,943	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000331:29,971–30,147	A	MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000331:81,667–81,879	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000331:81,667–81,879	A	MTLA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000227:24,795–24,938	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000533:7,288–11,743	A	MTLA1, MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000533:7,288–11,743	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000032:9,536–25,074	MATa	MATA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000032:9,536–25,074	A	MTLA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000189:60,343–60,480	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000431:123,843–124,004	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000369:28,499–28,657	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000264:3,546–3,707	undetermined	MATA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000264:50,327–50,485	A	MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000129:25,993–26,184	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000141:6,326–6,418	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000014:4,494–4,649	undetermined	MATA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000527:2,739–2,834	A	MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000527:42,027–42,197	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000439:67,923–68,024	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000531:9,375–9,467	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000285:17,386–17,484	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000376:13,220–25,235	undetermined	MATA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000376:13,220–25,235	A	MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000376:139,147–139,377	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000442:25,275–25,619	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000583:5,590–5,679	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000418:33,116–33,346	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000259:47,427–47,591	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000295:11,956–12,057	undetermined	MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000151:16,094–16,228	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000151:68,157–68,315	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000160:34,641–34,757	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000220:35,157–35,252	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000170:12,797–12,892	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000345:104,481–104,624	undetermined	MATALPHA2, MATA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000081:8,745–21,345	undetermined	MATA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000081:8,745–21,345	A	MTLA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000301:2,713–2,877	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000066:7,605–7,712	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000066:146,693–146,812	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000385:1,247–1,354	MATa	MATA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000342:5,178–5,273	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000408:40,160–57,439	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000408:40,160–57,439	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000161:4,626–4,808	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000396:38,327–38,467	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000078:28,555–28,656	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000547:44,572–44,769	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000435:6,573–6,689	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MATsc	SWFS01000156:3,836–4,081	undetermined	MATALPHA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000156:39,978–40,151	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000484:24,491–24,673	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000050:63,572–63,694	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000192:44,789–44,905	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000433:57,656–57,808	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000097:60,451–60,591	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MATsc	SWFS01000097:189,794–190,018	MATalpha	MATALPHA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000112:48,751–48,960	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000109:23,932–24,051	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000463:12,906–13,040	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000168:6,661–6,771	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000168:33,922–34,074	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000201:21,098–21,214	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000163:70,955–71,113	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000538:7,080–7,223	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000412:580–771	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000420:74,931–75,176	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000346:27,851–28,012	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000182:38,568–38,837	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000289:12,843–12,959	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000155:10,850–10,939	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000505:16,634–18,483	alpha	MTLalpha1, MTLalpha2	0	fewer than 2 genes could be modelled
MTL	SWFS01000137:29,739–29,945	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000378:4,428–4,598	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000157:80,446–80,577	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000306:15,727–15,840	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000410:4,544–4,654	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000122:46,525–46,635	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000082:63,110–63,223	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000354:8,613–8,873	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000236:49,283–49,375	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000043:10,035–10,217	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000123:121,349–121,468	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000391:2,301–2,630	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000515:2,330–25,766	A	MTLA2, MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000349:43,160–43,267	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000138:101–229	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000101:11,423–11,524	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000575:35,104–35,253	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000321:7,617–7,730	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000399:3,591–3,785	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000562:13,810–13,926	A	MTLA2	0	fewer than 2 genes could be modelled
MTL	SWFS01000221:18,932–19,024	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000046:360–581	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000093:152,884–153,120	alpha	MTLalpha1	0	fewer than 2 genes could be modelled
MTL	SWFS01000576:13,076–13,288	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000215:664–846	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000179:38,182–38,316	A	MTLA1	0	fewer than 2 genes could be modelled
MTL	SWFS01000011:40,619–46,654	undetermined	PIK1	1	too few of the family's genes found
MTL	SWFS01000027:5,004–6,539	undetermined	PAP1	1	too few of the family's genes found
MTL	SWFS01000088:149–1,441	undetermined	OBP1	1	too few of the family's genes found
MTL	SWFS01000317:76,769–77,977	undetermined	OBP1	1	too few of the family's genes found
MTL	SWFS01000379:587–3,460	undetermined	PIK1	1	too few of the family's genes found

Provenance

Genome file: TciferriiCBS4856.genome.fasta
Assembly: 583 contigs · 20.5 Mb · N50 69.0 kb
Genome SHA-256: 295b71f14d1659493babf671475f6b99eeb10e1d1b0421d63d53c2a2d038df65
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': 410830, '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 410830', 'routed_by': 'family taxid 410830 (phylum_fallback)'}, 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: 2026-11-07T01:53:34Z
Run time: 28 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.