MATPredict · mating-type report

AnidulansFGSCA4

MAT locus above the FungiDB annotation (gene by gene)

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 02:18 UTC by MATPredict 0.8.1

Result

Mating-type loci

MAT1-2high confidenceMAT1-1medium confidence

Called loci 2

MAT1-2 MAT family · Ascomycota

high confidence
Gene order of the MAT1-2 locus on ChrIII_A_nidulans_FGSC_A4MAT1-2 locus: genes from left to right on ChrIII_A_nidulans_FGSC_A4, 1,140,942 to 1,149,995: COX13 (conserved flank, minus strand); APN2 (conserved flank, plus strand); MAT1-1-3 (core MAT gene, minus strand); MAT1-2-1 (core MAT gene, minus strand).1,142 kb1,144 kb1,146 kb1,148 kb1,150 kb← 1,140.5 kb more to contig endcalled locusCOX13: conserved flank, 1,140,942–1,141,641 (-), identity 100.0%, search hit onlyCOX13APN2: conserved flank, 1,141,955–1,144,058 (+), identity 100.0%, search hit onlyAPN2MAT1-1-3: core MAT gene, 1,148,940–1,149,995 (-), identity 39.0%, search hit onlyMAT1-1-3 (lost to MAT1-2-1)MAT1-2-1: core MAT gene, 1,148,940–1,149,995 (-), identity 100.0%, search hit onlyMAT1-2-1
Gene order on ChrIII_A_nidulans_FGSC_A4. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on ChrIII_A_nidulans_FGSC_A4, 1,140,490 to 1,150,447AN10585 1,140,627-1,141,697 (-): Ortholog(s) have cytochrome-c oxidase activity, enzyme regulator activity, role in aerobic respiration, mitochondrial respiratory chain supercomplex assembly and mitochondrial respiratory chain complex IV, plasma membrane localizationAN10585AN4736 1,141,871-1,144,975 (+): Ortholog(s) have DNA-(apurinic or apyrimidinic site) lyase activity, double-stranded DNA 3'-5' exodeoxyribonuclease activity, phosphodiesterase I activityAN4736AN4735 1,144,946-1,147,883 (-): Ortholog of A. fumigatus Af293 : Afu3g06200, A. niger CBS 513.88 : An11g10210, Aspergillus wentii : Aspwe1_0060656, Aspergillus sydowii : Aspsy1_0056669 and Aspergillus terreus NIH2624 : ATET_08809AN4735AN4734 1,148,276-1,150,126 (-): HMG domain mating-type proteinAN4734 MAT2
FungiDB release 71 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
  • conserved flank
  • search hit only
  • MAT1-1-3 is a weak hit to the other idiomorph's gene and was not counted against the call.
Location
ChrIII_A_nidulans_FGSC_A4:1,140,942–1,149,995 · 9.1 kb
Own genes
ChrIII_A_nidulans_FGSC_A4:1,140,942–1,149,995 · 9.1 kb
Locus
Complete locus: MAT gene(s) with their flanking genes.
Genes modelled
3 of 4 gene hits
Nearest contig end
1.1 Mb
Region (samtools)
ChrIII_A_nidulans_FGSC_A4:1140942-1149995
Idiomorph scores
  • MAT1-2 621.0

Margin over the set-aside MAT1-1-3 hit: 61.0 identity points (the narrowest overlap resolution below).

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

Overlapping hits resolved

Where genes of two idiomorphs hit the same place, the stronger hit was kept.

keptidentity %set asideidentity %overlap %basis
MAT1-2-1100.0MAT1-1-339.0100.0higher identity

Gene evidence

GeneRoleModel Identity %E-value Position (strand)Exons Reference recordFungiDB gene
COX13conserved flankhit onlyDIAMOND, proteome100.0cov 87.3%6.4e-84235 bits1,140,942–1,141,641 -–162425_fgsc-a4_MAT_combinedAN10585
APN2conserved flankhit onlyDIAMOND, proteome100.0cov 100.0%< 1e-1801,251 bits1,141,955–1,144,058 +–162425_fgsc-a4_MAT_combinedAN4736
MAT1-1-3core MATother idiomorph, not countedlost to MAT1-2-1, not countedhit onlyDIAMOND, proteome39.0cov 42.8%8.5e-1564 bits1,148,940–1,149,995 -–230073_uamh-1363_MAT_MAT1-1AN4734 MAT2
MAT1-2-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%1.0e-230621 bits1,148,940–1,149,995 -–162425_fgsc-a4_MAT_combinedAN4734 MAT2
SLA2expected, not found–

MAT1-1 MAT family · Ascomycota

medium confidence
Gene order of the MAT1-1 locus on ChrVI_A_nidulans_FGSC_A4MAT1-1 locus: genes from left to right on ChrVI_A_nidulans_FGSC_A4, 2,903,571 to 2,910,117: SLA2 (conserved flank, plus strand); MAT1-1-1 (core MAT gene, minus strand).2,904 kb2,906 kb2,908 kb2,910 kb497.5 kb more to contig end →called locusSLA2: conserved flank, 2,903,571–2,907,134 (+), identity 100.0%, search hit onlySLA2MAT1-1-1: core MAT gene, 2,908,976–2,910,117 (-), identity 100.0%, search hit onlyMAT1-1-1
Gene order on ChrVI_A_nidulans_FGSC_A4. Scroll sideways to see the whole figure.
FungiDB release 71 gene models on ChrVI_A_nidulans_FGSC_A4, 2,903,244 to 2,910,444AN2756 2,903,537-2,907,752 (+): Predicted actin binding protein with similarity to Saccharomyces cerevisiae Sla2pAN2756 slaBAN2755 2,908,205-2,910,242 (-): Alpha-domain mating-type proteinAN2755 MAT1
FungiDB release 71 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
  • conserved flank
  • search hit only
Location
ChrVI_A_nidulans_FGSC_A4:2,903,571–2,910,117 · 6.5 kb
Own genes
ChrVI_A_nidulans_FGSC_A4:2,903,571–2,910,117 · 6.5 kb
Locus
Provisional: the call only tied the admission bar, or came from the relaxed pass.
Genes modelled
2 of 2 gene hits
Nearest contig end
497.8 kb
Region (samtools)
ChrVI_A_nidulans_FGSC_A4:2903571-2910117
Idiomorph scores
  • MAT1-1 719.0

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 recordFungiDB gene
SLA2conserved flankhit onlyDIAMOND, proteome100.0cov 94.5%< 1e-1801,478 bits2,903,571–2,907,134 +–162425_fgsc-a4_MAT_combinedAN2756 slaB
MAT1-1-1core MAThit onlyDIAMOND, proteome100.0cov 100.0%3.8e-268719 bits2,908,976–2,910,117 -–162425_fgsc-a4_MAT_combinedAN2755 MAT1
APN2expected, not found–
COX13expected, not found–

Withheld candidate loci 3

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 (3).

Show the 3 withheld loci

Withheld loci (3)

familylocationidiomorph genesmodelledreason
MATChrII_A_nidulans_FGSC_A4:3,437,098–3,442,942MAT1-1MAT1-2-1, MAT1-1-31too few of the family's genes found
MATChrII_A_nidulans_FGSC_A4:3,791,544–3,794,989MAT1-2MAT1-2-11too few of the family's genes found
MATChrVII_A_nidulans_FGSC_A4:2,398,827–2,401,084MAT1-2MAT1-2-11too few of the family's genes found

Provenance

Genome file
AnidulansFGSCA4.genome.fasta
Assembly
9 contigs · 30.5 Mb · N50 3.8 Mb
Genome SHA-256
a148c2161d7f5411c58af46fe3ec0411bc9a38c9a09a99076d8fd600fe80d46f
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': 'genus', 'routing_taxid': 1131492, '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 1131492', 'routed_by': 'family taxid 1131492 (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
2026-11-07T02:17:20Z
Run time
70 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