Wheat genes, Watkins pangenome, EMS mutants, expression, genotypes, germplasm and papers (WheatIS)
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Phenotyping studies (field and glasshouse trials) with trait data for a wheat line, live from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/title case are tried too, e.g. 'Soissons' -> 'SOISSONS'). Returns the matching germplasm records (source, holding institute, accession) and each study's name, trial/network, season, location, number of observations, variables measured and link. Use brapi_observations for the trait values.
Pick your client. Values in capitals, like YOUR_TOKEN, are yours to fill in.
Run in a terminal
claude mcp add --transport http askwheat https://askwheat.plantdatabases.org/mcp
Phenotyping studies (field and glasshouse trials) with trait data for a wheat line, live from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE). germplasm: a cultivar or line name (matched exactly; upper/title case are tried too, e.g. 'Soissons' -> 'SOISSONS'). Returns the matching germplasm records (source, holding institute, accession) and each study's name, trial/network, season, location, number of observations, variables measured and link. Use brapi_observations for the trait values.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| germplasm* | string |
{
"type": "object",
"title": "brapi_germplasm_studiesArguments",
"required": [
"germplasm"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"germplasm": {
"type": "string",
"title": "Germplasm"
}
}
}Trait observations for a wheat line from the BrAPI nodes (currently the INRAE wheat trial network and Whealbi trials in GnpIS, served through FAIDARE), summarised per study and variable: n, mean, min, max (numeric values) or the distinct values, season and location. germplasm: line name (as in brapi_germplasm_studies). trait filters variables by name or ontology ID part (e.g. 'rdt', 'CO_321:1000074', 'yield'; INRAE short names are glossed: rdt = grain yield, prot = grain protein, pmg = thousand-grain weight, ht = plant height, rj/rb = yellow/brown rust). study filters by study name part (e.g. 'Le_Moulon', '2015'). Compare values within a study.
| Argument | Type | Description |
|---|---|---|
| study | any | |
| trait | any | |
| germplasm* | string |
{
"type": "object",
"title": "brapi_observationsArguments",
"required": [
"germplasm"
],
"properties": {
"study": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Study",
"default": null
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"germplasm": {
"type": "string",
"title": "Germplasm"
}
}
}What askWheat currently indexes: record counts per database and data type, and data versions.
No arguments.
{
"type": "object",
"title": "data_sourcesArguments",
"properties": {}
}Bread wheat RNA-seq experiments held by askWheat (Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat)): baseline (TPM by tissue / developmental stage / treatment) and differential (stress, pathogen, genotype contrasts). query filters descriptions/labels (e.g. 'drought', 'grain', 'Fusarium'). Gives each experiment's assay groups (baseline) or contrasts (differential).
| Argument | Type | Description |
|---|---|---|
| query | any |
{
"type": "object",
"title": "expression_experimentsArguments",
"properties": {
"query": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Query",
"default": null
}
}
}Genes characteristic of a tissue/stage or responsive to a treatment in one Expression Atlas experiment. Baseline experiment + group (text matched to group labels, e.g. 'root', 'grain'): genes with TPM >= min_tpm in a matching group ranked by specificity = (max TPM in matching groups + 1) / (max TPM in other groups + 1). Differential experiment + contrast (text matched to contrast names or IDs): significant genes, direction 'up' or 'down', ranked by |log2FC|. Use expression_experiments() for group and contrast names.
| Argument | Type | Description |
|---|---|---|
| group | any | |
| limit | integer | |
| min_tpm | number | |
| contrast | any | |
| direction | string | |
| experiment* | string |
{
"type": "object",
"title": "expression_genesArguments",
"required": [
"experiment"
],
"properties": {
"group": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Group",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"min_tpm": {
"type": "number",
"title": "Min Tpm",
"default": 5
},
"contrast": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Contrast",
"default": null
},
"direction": {
"type": "string",
"title": "Direction",
"default": "up"
},
"experiment": {
"type": "string",
"title": "Experiment"
}
}
}Find wheat accessions/cultivars/lines by name or accession ID across five indexed sources: CropSNPdb (SNP-genotyped lines, incl. all Australian Grains Genebank wheat and CAIGE breeding lines), the Watkins Wheat Pangenome (sequenced landraces), OzWheat (CSIRO GWAS panel lines), FAIDARE (INRAE GnpIS collections, e.g. the FRA040 Clermont-Ferrand wheat collection, and EVA European genebank evaluation sets) and genebank accessions of Triticum and Aegilops from GBIF (holding genebank as FAO WIEWS code, e.g. MEX002 = CIMMYT, accession number; mostly Svalbard safety duplicates).
| Argument | Type | Description |
|---|---|---|
| name* | string | |
| limit | integer |
{
"type": "object",
"title": "find_germplasmArguments",
"required": [
"name"
],
"properties": {
"name": {
"type": "string",
"title": "Name"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 10
}
}
}Position(s) of a genetic marker (90K/80K/9K iSelect, 35K Axiom, KASP, DArT, SSR e.g. 'BS00000713', 'wmc617', 'Xgwm149'; 40K array IDs such as 'IWB61980' or 'AVRIG14047' come from CropSNPdb) on IWGSC RefSeq v2.1 (IWGSC GMAP alignments), with genes within +/- flank bp of each hit.
| Argument | Type | Description |
|---|---|---|
| flank | integer | |
| marker* | string |
{
"type": "object",
"title": "find_markerArguments",
"required": [
"marker"
],
"properties": {
"flank": {
"type": "integer",
"title": "Flank",
"default": 100000
},
"marker": {
"type": "string",
"title": "Marker"
}
}
}Where and when a wheat gene is expressed, and under which treatments it changes, from Expression Atlas and SRA study SRP045409 (seedling drought, heat and combined stress; quantified by askWheat). gene: symbol or any IWGSC RefSeq ID (converted to v1.1, as used by Atlas). Baseline: TPM (median over replicates, with range) for the top_groups highest-expressed tissues/stages per experiment. Differential: every contrast where the gene is significant (adjusted p < 0.05, |log2FC| >= 1). experiment restricts to one accession.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| experiment | any | |
| top_groups | integer |
{
"type": "object",
"title": "gene_expressionArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"experiment": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Experiment",
"default": null
},
"top_groups": {
"type": "integer",
"title": "Top Groups",
"default": 10
}
}
}IWGSC RefSeq v2.1 functional annotation (InterPro, Pfam, Gene Ontology) for a gene symbol or any-version IWGSC ID. annotation_types filters e.g. ['Gene Ontology'] or ['Pfam','InterPro'].
| Argument | Type | Description |
|---|---|---|
| identifier* | string | |
| annotation_types | any |
{
"type": "object",
"title": "gene_functionArguments",
"required": [
"identifier"
],
"properties": {
"identifier": {
"type": "string",
"title": "Identifier"
},
"annotation_types": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"title": "Annotation Types",
"default": null
}
}
}Plant Reactome metabolic and signalling pathways of a gene (Gramene), with the top-level category and a link to the pathway diagram. gene: an Ensembl Plants gene ID or a gene name/symbol. Pathways are projected from rice by orthology, so say they are inferred. Use pathway_genes for the reverse (all genes of a pathway).
| Argument | Type | Description |
|---|---|---|
| gene* | string |
{
"type": "object",
"title": "gene_pathwaysArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
}
}
}Field phenotypes of wheat cultivars and genebank accessions from IPK e!DAL (CC BY 4.0). Datasets: 'GABI-WHEAT' (372 European elite cultivars 1975-2007; 16 traits incl. grain yield, heading, height, TKW, protein, sedimentation, falling number, FHB, Septoria, tan spot; BLUEs per trial environment and across 2009-2010 trials in Germany/France), 'IPK' (12,754 IPK genebank accessions, TRI numbers: flowering time, plant height, TKW, BLUEs across 70 years of regeneration), 'EU-GENEBANKS' (about 40,000 accessions of CREA, ICARDA, IHAR, INIA, IPGR, NARDI, NPPC, Agroscope: heading, height, TKW, some disease, protein and yield). No arguments lists datasets and traits. query: a cultivar name or accession number (e.g. 'Julius', 'TRI 1000', 'IG 107099') -> all its trait values. trait (+ order 'high'/'low'): rank accessions of one dataset. filters: several traits at once, e.g. 'plant height < 90; thousand kernel weight > 45' (BLUEs, one dataset). genebank: FAO code or name (LBN002, CREA); country: origin (IPK dataset).
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| order | string | |
| query | any | |
| trait | any | |
| country | any | |
| dataset | any | |
| filters |
List IWGSC genes overlapping a region. chromosome like '7D'; assembly 'v2.1' (RefSeq v2.1 coordinates) or 'v1.0' (RefSeq v1.0 coordinates, v1.1 gene IDs). Region size is capped at 20 Mb.
| Argument | Type | Description |
|---|---|---|
| end* | integer | |
| limit | integer | |
| start* | integer | |
| assembly | string | |
| chromosome* | string |
{
"type": "object",
"title": "genes_in_regionArguments",
"required": [
"chromosome",
"start",
"end"
],
"properties": {
"end": {
"type": "integer",
"title": "End"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"start": {
"type": "integer",
"title": "Start"
},
"assembly": {
"type": "string",
"title": "Assembly",
"default": "v2.1"
},
"chromosome": {
"type": "string",
"title": "Chromosome"
}
}
}Full record for one paper: DOI (10.xxxx/..), PMID (digits) or PMCID (PMC...). Returns the abstract, open-access status and full-text links.
| Argument | Type | Description |
|---|---|---|
| identifier* | string |
{
"type": "object",
"title": "get_paperArguments",
"required": [
"identifier"
],
"properties": {
"identifier": {
"type": "string",
"title": "Identifier"
}
}
}OzWheat diversity panel lines (285 Australian and international cultivars and breeding lines): name, OzWheat ID, Australian Grains Genebank (AGG) accession, pedigree and phenotype BLUEs (days to anthesis/heading, degree-days to heading, height per trial). query matches name, OzWheat ID (oz0001), AGG number or pedigree words. marker (an OzWheat MTA peak SNP such as 'SNP34815_7B', from ozwheat_mtas) with allele lists the lines carrying that allele. include_genotypes adds each line's calls at all MTA peak markers. Lines are also often in CropSNPdb under the same cultivar name (use snp_lines).
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query | any | |
| allele | any | |
| marker | any | |
| include_genotypes | boolean |
{
"type": "object",
"title": "ozwheat_linesArguments",
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 30
},
"query": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Query",
"default": null
},
"allele": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Allele",
"default": null
},
"marker": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Marker",
"default": null
},
"include_genotypes": {
"type": "boolean",
"title": "Include Genotypes",
"default": false
}
}
}Marker-trait associations from the OzWheat GWAS (285 Australian and international wheat cultivars and lines; glasshouse 2016 and field trials at Canberra 2018-19, Wagga 2018, Narrabri 2019). Traits: days to anthesis, days to heading, degree-days to heading ('flowering'/'heading') and plant height. Filter by trait, gene (symbol or any IWGSC ID; matches the gene carrying the SNP or the linked candidate gene, or the name in their annotation) and/or region (chromosome like '7B' with start/end in RefSeq v1.0 bp). Each MTA gives the peak SNP and its position, p-value, the gene it sits in (with v1.1/v2.1 IDs), any literature candidate gene, and the allele effect: trait mean (BLUE) of lines carrying each allele in that trial.
| Argument | Type | Description |
|---|---|---|
| end | any | |
| gene | any | |
| limit | integer | |
| start | any | |
| trait | any | |
| chromosome | any |
{
"type": "object",
"title": "ozwheat_mtasArguments",
"properties": {
"end": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "End",
"default": null
},
"gene": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"start": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Start",
"default": null
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"chromosome": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chromosome",
"default": null
}
}
}Genes in a Plant Reactome pathway: pathway is a name or words from it ('jasmonic acid biosynthesis', 'gibberellin', 'flavonoid') or a stable ID (R-TAE-1119332). species: a species name as Plant Reactome writes it ('Triticum aestivum', 'Brassica napus', 'Glycine max'); default all species loaded for this site. Matching pathways are listed with their genes per species. Membership is projected from rice by orthology.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| pathway* | string | |
| species | any |
{
"type": "object",
"title": "pathway_genesArguments",
"required": [
"pathway"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"pathway": {
"type": "string",
"title": "Pathway"
},
"species": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Species",
"default": null
}
}
}Resolve a wheat gene symbol (e.g. Lr34, Rht-B1) or IWGSC gene ID in any RefSeq version (v1.0 TraesCS..01G, v1.1 TraesCS..02G, v2.1 TraesCS..03G, CSS2014 Traes_..) to all versions, genomic locations, curated symbol/trait (with verification status), Watkins pangenome presence and links.
| Argument | Type | Description |
|---|---|---|
| identifier* | string |
{
"type": "object",
"title": "resolve_geneArguments",
"required": [
"identifier"
],
"properties": {
"identifier": {
"type": "string",
"title": "Identifier"
}
}
}Full-text search across all askWheat resources (genes, germplasm, genotyping datasets, files). Filters (exact values): database e.g. 'Ensembl Plants', 'Watkins Wheat Pangenome', 'CropSNPdb', 'GBIF genebank accessions'; entry_type e.g. 'Gene annotation', 'Germplasm', 'Genotyping Experiment', 'File'; species e.g. 'Triticum aestivum'. Returns total count, facet counts and the top hits with source URLs.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string | |
| species | any | |
| database | any | |
| entry_type | any |
{
"type": "object",
"title": "search_dataArguments",
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 10
},
"query": {
"type": "string",
"title": "Query"
},
"species": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Species",
"default": null
},
"database": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Database",
"default": null
},
"entry_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Entry Type",
"default": null
}
}
}Search publications and preprints in Europe PMC (PubMed, PMC, bioRxiv and others). query: free text or Europe PMC syntax (e.g. 'grain size QTL 6A', 'TITLE:"pan-genome"'). gene: optional gene symbol or IWGSC ID; its curated synonyms and RefSeq IDs are OR-ed into the query (e.g. gene='Lr34' also matches Yr18, Sr57, TraesCS7D02G080300). Words are matched in title and abstract; full_text=True also searches open-access full text. crop_only requires wheat/Triticum/Aegilops in title or abstract. sort: 'relevance', 'date' (newest first) or 'cited'. Returns hit count and papers with DOI/PMID, year, journal, open-access flag, citations and a short abstract.
| Argument | Type | Description |
|---|---|---|
| gene | any | |
| sort | string | |
| limit | integer | |
| query* | string | |
| crop_only | boolean | |
| from_year | any | |
| full_text | boolean | |
| open_access_only | boolean |
Compare two lines' SNP genotypes on a chromosome (optionally a region): markers compared, identical, different, % identity and the regions where they differ (useful for pedigree/introgression questions).
| Argument | Type | Description |
|---|---|---|
| end | any | |
| start | any | |
| line_a* | string | |
| line_b* | string | |
| dataset | string | |
| chromosome* | string |
{
"type": "object",
"title": "snp_compare_linesArguments",
"required": [
"line_a",
"line_b",
"chromosome"
],
"properties": {
"end": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "End",
"default": null
},
"start": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "Start",
"default": null
},
"line_a": {
"type": "string",
"title": "Line A"
},
"line_b": {
"type": "string",
"title": "Line B"
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat40k"
},
"chromosome": {
"type": "string",
"title": "Chromosome"
}
}
}SNP genotype calls for up to 50 lines in a region (chromosome like '2D'). Returns markers with positions and each line's call. Keep regions small (a few Mb) for many lines.
| Argument | Type | Description |
|---|---|---|
| end | integer | |
| lines* | array | |
| start | integer | |
| dataset | string | |
| chromosome* | string |
{
"type": "object",
"title": "snp_genotypesArguments",
"required": [
"lines",
"chromosome"
],
"properties": {
"end": {
"type": "integer",
"title": "End",
"default": 1000000000
},
"lines": {
"type": "array",
"items": {
"type": "string"
},
"title": "Lines"
},
"start": {
"type": "integer",
"title": "Start",
"default": 1
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat40k"
},
"chromosome": {
"type": "string",
"title": "Chromosome"
}
}
}Lines that share a reference line's SNP haplotype in a region (max 5 Mb), e.g. which genebank lines carry the Cadenza haplotype around a gene. Only markers polymorphic in the panel (minor allele frequency >= min_maf) are used, and a match needs calls at >= min_called of them with at most max_mismatch differences. Always report informative_markers and fraction_matching; if 'note' says the haplotype is common, say it is not diagnostic.
| Argument | Type | Description |
|---|---|---|
| end* | integer | |
| line* | string | |
| limit | integer | |
| start* | integer | |
| dataset | string | |
| min_maf | number | |
| chromosome* | string | |
| min_called | number | |
| max_mismatch | integer |
Find SNP-genotyped lines in CropSNPdb by name or AGG accession (e.g. 'Cadenza', 'AGG 38862', 'CAIGE ZWB17' or a CAIGE GID '7396745'). Returns line name, accession(s), country, pedigree, status, breeding organisation and donor. dataset: 'wheat40k' (default) or 'wheat90k'.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string | |
| dataset | string |
{
"type": "object",
"title": "snp_linesArguments",
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"query": {
"type": "string",
"title": "Query"
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat40k"
}
}
}SNP array markers (IDs and positions) in a region, with the total count.
| Argument | Type | Description |
|---|---|---|
| end* | integer | |
| limit | integer | |
| start* | integer | |
| dataset | string | |
| chromosome* | string |
{
"type": "object",
"title": "snp_markersArguments",
"required": [
"chromosome",
"start",
"end"
],
"properties": {
"end": {
"type": "integer",
"title": "End"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"start": {
"type": "integer",
"title": "Start"
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat40k"
},
"chromosome": {
"type": "string",
"title": "Chromosome"
}
}
}Field trial trait data held in CropSNPdb for this crop (T3 trials with Crop Ontology trait IDs, Australian Grains Genebank records). With no arguments, lists the available traits. Filter by line and/or trait: trait matches the exact name or any part of it (e.g. 'Height', 'grain yield'). Most phenotyped lines are in the wheat90k dataset.
| Argument | Type | Description |
|---|---|---|
| line | any | |
| limit | integer | |
| trait | any | |
| dataset | string |
{
"type": "object",
"title": "snp_phenotypesArguments",
"properties": {
"line": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Line",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat90k"
}
}
}Trait-associated positions across the genome for a chromosome overview: GWAS marker-trait associations and peaks, named trait genes and mapped trait loci held by this site, with chromosome sizes, each with a genome browser link where the assembly is loaded. trait: words to match (e.g. 'height', 'oil', 'alkaloid'); chromosome filters one chromosome. Map marker tracks are left out unless a chromosome is given.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| trait | any | |
| chromosome | any |
{
"type": "object",
"title": "trait_hitsArguments",
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 300
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"chromosome": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chromosome",
"default": null
}
}
}One Watkins accession (e.g. WATDE0063, or a synonym): origin, ancestral group, coordinates, Seedstor link, number of genes present, presence/absence of the listed genes (symbols or any IWGSC IDs accepted), all its phenotype records (trial, trait, value, units) and any RIL populations it is a parent of.
| Argument | Type | Description |
|---|---|---|
| name* | string | |
| genes | any |
{
"type": "object",
"title": "watkins_accessionArguments",
"required": [
"name"
],
"properties": {
"name": {
"type": "string",
"title": "Name"
},
"genes": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"title": "Genes",
"default": null
}
}
}Genes with a predicted loss-of-function allele (stop gained, start/stop lost, splice site) in one Watkins landrace or modern cultivar (WatSeq). accession: Watkins store code or WatSeq sample name (e.g. 'Watkins 1190027', 'WATDE0027', 'Paragon'). genes optionally restricts to a gene list (symbols or IWGSC IDs). Rare alleles (carried by few accessions) are listed first.
| Argument | Type | Description |
|---|---|---|
| genes | any | |
| limit | integer | |
| accession* | string | |
| homozygous_only | boolean |
{
"type": "object",
"title": "watkins_accession_lofArguments",
"required": [
"accession"
],
"properties": {
"genes": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"title": "Genes",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 500
},
"accession": {
"type": "string",
"title": "Accession"
},
"homozygous_only": {
"type": "boolean",
"title": "Homozygous Only",
"default": true
}
}
}Genes whose presence frequency differs most between two sets of Watkins accessions. group_a / group_b as '<field>:<value>' with field one of group (ancestral group), country, continent, growth_habit, e.g. 'group:AG3' vs 'group:Modern', 'country:India' vs 'country:China'. min_diff is the minimum absolute frequency difference (0-1). Negative diff = more common in group_b.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| group_a* | string | |
| group_b* | string | |
| min_diff | number |
{
"type": "object",
"title": "watkins_compare_groupsArguments",
"required": [
"group_a",
"group_b"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"group_a": {
"type": "string",
"title": "Group A"
},
"group_b": {
"type": "string",
"title": "Group B"
},
"min_diff": {
"type": "number",
"title": "Min Diff",
"default": 0.5
}
}
}Find Watkins pangenome genes by UniProt protein name, gene name, protein family or ID fragment (e.g. 'FAR1', 'NLR', 'Disease resistance protein RGA'). Returns gene IDs with UniProt/GO annotation.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| query* | string |
{
"type": "object",
"title": "watkins_find_genesArguments",
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 25
},
"query": {
"type": "string",
"title": "Query"
}
}
}Watkins accessions that carry (present=True) or lack (present=False) a gene, optionally filtered by country, continent, ancestral_group (AG1-AG7 or Modern) or growth_habit. Returns metadata, coordinates and Seedstor ordering links.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| limit | integer | |
| offset | integer | |
| country | any | |
| present | boolean | |
| continent | any | |
| growth_habit | any | |
| ancestral_group | any |
{
"type": "object",
"title": "watkins_gene_accessionsArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"offset": {
"type": "integer",
"title": "Offset",
"default": 0
},
"country": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Country",
"default": null
},
"present": {
"type": "boolean",
"title": "Present",
"default": true
},
"continent": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Continent",
"default": null
},
"growth_habit": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Growth Habit",
"default": null
},
"ancestral_group": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Ancestral Group",
"default": null
}
}
}Haplotypes of a gene across the Watkins landraces and modern cultivars (WatSeq, 1,051 accessions). 'snp' (default where built): accessions grouped by their SNP alleles in the gene +-2 kb (MAF >= 0.02), each haplotype with its coding changes (e.g. p.Arg134Gln), whether it is Chinese Spring-like, size and frequency by ancestral group (AG1-AG7, Modern) and country; 'ibspy': the IBSpy haplotype group of the 1 Mb block holding the gene, with the pangenome assemblies (e.g. jagger-pg, mace-pg) that share each block haplotype. Accessions lacking the gene in the Watkins pangenome are listed as 'absent'. gene: symbol or any IWGSC ID (positions RefSeq v1.0).
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| source | string | |
| members | integer |
{
"type": "object",
"title": "watkins_gene_haplotypesArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"source": {
"type": "string",
"title": "Source",
"default": "auto"
},
"members": {
"type": "integer",
"title": "Members",
"default": 30
}
}
}Presence/absence of one gene across the 1,038 Watkins pangenome accessions: present count, core/variable, counts by ancestral group (AG1-AG7, Modern), continent and growth habit, UniProt/GO annotation and links. gene: symbol, any IWGSC RefSeq ID, or a pangenome gene-model ID.
| Argument | Type | Description |
|---|---|---|
| gene* | string |
{
"type": "object",
"title": "watkins_gene_presenceArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
}
}
}Compare a trait between Watkins accessions that carry vs lack a gene, per trial: n, mean and median per group and a Mann-Whitney p-value (exploratory; no correction for population structure). gene: symbol, any IWGSC RefSeq ID or pangenome gene-model ID. trait: exact name from watkins_phenotypes (e.g. 'Heading time').
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| trait* | string | |
| trial | any |
{
"type": "object",
"title": "watkins_gene_traitArguments",
"required": [
"gene",
"trait"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"trait": {
"type": "string",
"title": "Trait"
},
"trial": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trial",
"default": null
}
}
}Trait values per haplotype of a gene (watkins_gene_haplotypes) in each Watkins trial: n, mean and median per haplotype and a Kruskal-Wallis test across haplotypes with >= min_n accessions. Exploratory: no correction for population structure or multiple testing, so a difference can reflect ancestry rather than the gene. trait: exact name from watkins_phenotypes (e.g. 'Heading time'); trial optional (all trials otherwise). include_values adds each accession's mean per haplotype (for plotting).
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| min_n | integer | |
| trait* | string | |
| trial | any | |
| source | string | |
| include_values | boolean |
{
"type": "object",
"title": "watkins_haplotype_traitArguments",
"required": [
"gene",
"trait"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"min_n": {
"type": "integer",
"title": "Min N",
"default": 5
},
"trait": {
"type": "string",
"title": "Trait"
},
"trial": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trial",
"default": null
},
"source": {
"type": "string",
"title": "Source",
"default": "auto"
},
"include_values": {
"type": "boolean",
"title": "Include Values",
"default": false
}
}
}Watkins landraces and modern cultivars carrying a predicted loss-of-function allele of a gene (WatSeq, 1,051 accessions): each stop-gained, start/stop-lost or splice-site SNP with its protein change, the number of homozygous and heterozygous carriers, and the carriers (accession, ancestral group, country) for ordering from the JIC Germplasm Resources Unit. gene: symbol or any IWGSC ID; homoeologues are listed for checking redundancy.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| carriers | integer |
{
"type": "object",
"title": "watkins_lof_allelesArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"carriers": {
"type": "integer",
"title": "Carriers",
"default": 100
}
}
}Genes inside the Watkins introgression of a TK-NIL (Watkins segment in a Paragon background), with presence in the Watkins donor and frequency in modern cultivars and landraces. nil_line is a NIL line name from watkins_population_phenotypes (e.g. 'ParW141_0016-7-10-Q2D-Hd-P'). The interval comes from the NIL name (chromosome-start-end on RefSeq v1.0). Highlights genes the donor lacks but most modern cultivars carry, and genes the donor carries but most modern cultivars lack (Paragon itself is not in the pangenome).
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| nil_line* | string |
{
"type": "object",
"title": "watkins_nil_genesArguments",
"required": [
"nil_line"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 300
},
"nil_line": {
"type": "string",
"title": "Nil Line"
}
}
}Field/glasshouse phenotypes of Watkins accessions (heading, height, grain size/weight/quality, senescence, lodging, rust and mildew scores, morphology). With no arguments, lists the trials (JIC UK 2006-2020, Egypt 2019-2021, Limagrain seedling yellow rust 2020, Kenya/Ethiopia rust 2013) and trait names with units. Filter by accession (e.g. WATDE0063), exact trait name, trial and/or country.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| trait | any | |
| trial | any | |
| country | any | |
| accession | any |
{
"type": "object",
"title": "watkins_phenotypesArguments",
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"trial": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trial",
"default": null
},
"country": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Country",
"default": null
},
"accession": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Accession",
"default": null
}
}
}Trial phenotypes (line means per trial) of Paragon x Watkins RILs and TK-NILs: heading, height, yield, grain traits, biomass, N content and more from JIC, Rothamsted and Nottingham trials (2011-2022). population_type 'RIL', 'NIL' or 'check' (parents and controls, e.g. Paragon). line matches by prefix (e.g. 'ParW034_0012' also returns NILs derived from it). With no arguments, lists trials and traits.
| Argument | Type | Description |
|---|---|---|
| line | any | |
| limit | integer | |
| trait | any | |
| trial | any | |
| population | any | |
| watkins_parent | any | |
| population_type | any |
{
"type": "object",
"title": "watkins_population_phenotypesArguments",
"properties": {
"line": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Line",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"trial": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trial",
"default": null
},
"population": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Population",
"default": null
},
"watkins_parent": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Watkins Parent",
"default": null
},
"population_type": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Population Type",
"default": null
}
}
}Paragon x Watkins (and a few Robigus/other x Watkins) RIL populations: Watkins parent, country, ancestral group, number of RILs, GRU seed code, genetic map type and whether it donated TK-NILs. With population (e.g. 'ParW034') or watkins_parent (e.g. 'WATDE0005') also lists the trials in which its lines were phenotyped.
| Argument | Type | Description |
|---|---|---|
| population | any | |
| watkins_parent | any |
{
"type": "object",
"title": "watkins_populationsArguments",
"properties": {
"population": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Population",
"default": null
},
"watkins_parent": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Watkins Parent",
"default": null
}
}
}Which variable genes differ in presence between Watkins accessions with high vs low values of a trait in one trial (e.g. late vs early heading). Accessions are split into top/bottom quartile (split: quartile, tercile, median) within each ancestral group (stratify_by_group) and every variable gene is tested (Cochran-Mantel-Haenszel, Benjamini-Hochberg FDR). direction 'high' = genes more frequent in high-trait accessions, 'low' the reverse. trait and trial are exact names from watkins_phenotypes(). Exploratory screen, not a GWAS.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| split | string | |
| trait* | string | |
| trial* | string | |
| direction | string | |
| stratify_by_group | boolean |
{
"type": "object",
"title": "watkins_trait_genesArguments",
"required": [
"trait",
"trial"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 50
},
"split": {
"type": "string",
"title": "Split",
"default": "quartile"
},
"trait": {
"type": "string",
"title": "Trait"
},
"trial": {
"type": "string",
"title": "Trial"
},
"direction": {
"type": "string",
"title": "Direction",
"default": "both"
},
"stratify_by_group": {
"type": "boolean",
"title": "Stratify By Group",
"default": true
}
}
}Catalogue of Gene Symbols for Wheat (McIntosh et al., GrainGenes; 2024 edition): the official register of designated wheat genes and alleles. query: a gene or allele symbol ('Lr34', 'Rht-B1b'), locus ('Rht-B1' lists all its alleles), old synonym ('Rht1', 'Ppd1', 'NAM-B1'), trait words matching a catalogue section ('stem rust', 'height', 'vernalization', 'glutenin') or any text (a cultivar, marker or stock name). chromosome filters by arm or chromosome ('2D', '7DS'). Each entry gives its section, synonyms, chromosome, the catalogue text (stocks i:/v:, markers ma:, cloning c:) and, with full, the cited references resolved. Use resolve_gene for the IWGSC gene ID of cloned genes.
| Argument | Type | Description |
|---|---|---|
| full | boolean | |
| limit | integer | |
| query* | string | |
| chromosome | any |
{
"type": "object",
"title": "wheat_gene_catalogueArguments",
"required": [
"query"
],
"properties": {
"full": {
"type": "boolean",
"title": "Full",
"default": true
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 20
},
"query": {
"type": "string",
"title": "Query"
},
"chromosome": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chromosome",
"default": null
}
}
}Interactive gene view for one bread wheat gene: a relationship map of its A/B/D homoeologues, orthologues (durum, Ae. tauschii, barley, rice, maize, Arabidopsis and others), EMS knockout lines per copy, Watkins haplotypes, expression responses and recent papers, with tabs for mutations along the gene and the haplotype map. Clients that support MCP Apps show it in the chat; the result also lists the nodes and the askWheat gene page link (page) to share. gene: symbol or any IWGSC ID.
| Argument | Type | Description |
|---|---|---|
| gene* | string |
{
"type": "object",
"title": "wheat_gene_viewArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
}
}
}Relative expression of a wheat gene's A, B and D homoeologues per tissue/stage (Expression Atlas baseline experiments), with the homoeologue expression balance category of each tissue: balanced, A/B/D dominant or A/B/D suppressed, by distance to the ideal proportions (Ramirez-Gonzalez et al. 2018). Categories are given only for 1:1:1 triads with summed TPM >= 0.5. experiment restricts to one accession.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| experiment | any |
{
"type": "object",
"title": "wheat_homoeologue_expressionArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"experiment": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Experiment",
"default": null
}
}
}Homoeologues (the A/B/D copies), and orthologues in other grasses and Arabidopsis, of a bread wheat gene from Ensembl Plants Compara gene trees. gene: symbol or any IWGSC ID (converted to RefSeq v1.1). By default orthologues are listed for durum and wild emmer, T. urartu, Ae. tauschii, rye, barley, oat, Brachypodium, rice, maize, sorghum and Arabidopsis; target_species takes Ensembl names instead (e.g. ['triticum_aestivum_mace', 'hordeum_vulgare_goldenpromise'] for pan-genome cultivars). include_paralogues adds within-wheat paralogues (same-genome duplicates). Relationships: homoeolog_one2one, ortholog_one2one/one2many/many2many.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| target_species | any | |
| include_paralogues | boolean |
{
"type": "object",
"title": "wheat_homologuesArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"target_species": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"title": "Target Species",
"default": null
},
"include_paralogues": {
"type": "boolean",
"title": "Include Paralogues",
"default": false
}
}
}Which genes have EMS alleles in every homoeologue, i.e. can be knocked out across A, B and D by crossing Cadenza/Kronos lines. For each gene (genes: up to 300 symbols or IWGSC IDs, or region: RefSeq v1.0 interval up to 10 Mb, e.g. a QTL) the A/B/D copies come from Ensembl Compara, and each copy gets its lines with a consequence 'truncating' (default; stop, splice donor/acceptor, start/stop lost) or 'missense' etc. Status 'all_copies', 'partial' or 'none'; complete_only keeps 'all_copies'. Kronos lines cover only A and B copies; D copies need Cadenza. Lines hitting two copies at once are flagged.
| Argument | Type | Description |
|---|---|---|
| genes | any | |
| limit | integer | |
| region | any | |
| consequence | string | |
| complete_only | boolean |
{
"type": "object",
"title": "wheat_knockout_screenArguments",
"properties": {
"genes": {
"anyOf": [
{
"type": "array",
"items": {
"type": "string"
}
},
{
"type": "null"
}
],
"title": "Genes",
"default": null
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 100
},
"region": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Region",
"default": null
},
"consequence": {
"type": "string",
"title": "Consequence",
"default": "truncating"
},
"complete_only": {
"type": "boolean",
"title": "Complete Only",
"default": false
}
}
}Every mutation Ensembl lists for one EMS line (Cadenza or Kronos exome-capture TILLING; Krasileva et al. 2017), e.g. 'Cadenza1166' or 'Kronos2235': counts by consequence, the genes with truncating mutations, and the mutations (gene, consequence, amino-acid change, RefSeq v1.0 position), most severe first. consequence filters as in wheat_mutants ('truncating', 'missense', ...); chromosome e.g. '6D'. Use it to judge a line's background load and to check for off-target hits near a gene of interest before crossing.
| Argument | Type | Description |
|---|---|---|
| line* | string | |
| limit | integer | |
| chromosome | any | |
| consequence | any |
{
"type": "object",
"title": "wheat_mutant_lineArguments",
"required": [
"line"
],
"properties": {
"line": {
"type": "string",
"title": "Line"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"chromosome": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Chromosome",
"default": null
},
"consequence": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Consequence",
"default": null
}
}
}Induced mutations and natural variants in and around a bread wheat gene. source 'ems' (default): EMS mutant lines of tetraploid Kronos and hexaploid Cadenza with exome-capture sequencing (Krasileva et al. 2017; 2,735 lines), giving the line ID to order, e.g. Cadenza1158; 'diversity': exome-capture variants of 890 landraces and cultivars (He et al. 2019) and 103 Watkins landraces; 'all'. Every variant Ensembl assigns to the gene is kept: coding, splice, UTR, intron and upstream/downstream (within 5 kb). consequence filters: 'truncating' (stop gained, splice donor/acceptor, start/stop lost), 'missense', 'coding', 'splice', 'utr', 'intron', 'flanking' (upstream/downstream), 'regulatory' (flanking + UTR) or a Sequence Ontology term. homoeologues=True adds the A/B/D copies (to stack knockouts). gene: symbol or any IWGSC ID (converted to RefSeq v1.1); positions are RefSeq v1.0.
| Argument | Type | Description |
|---|---|---|
| gene* | string | |
| limit | integer | |
| source | string | |
| consequence | any | |
| homoeologues | boolean |
{
"type": "object",
"title": "wheat_mutantsArguments",
"required": [
"gene"
],
"properties": {
"gene": {
"type": "string",
"title": "Gene"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 100
},
"source": {
"type": "string",
"title": "Source",
"default": "ems"
},
"consequence": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Consequence",
"default": null
},
"homoeologues": {
"type": "boolean",
"title": "Homoeologues",
"default": false
}
}
}EMS mutations and exome-capture variants in a bread wheat interval on IWGSC RefSeq v1.0, including intergenic ones (promoters, unannotated regions, off-target capture). region: 'chr:start-end', e.g. '3A:100000000-100500000' (max 5 Mb). source 'ems', 'diversity' or 'all' (default); consequence as in wheat_mutants, plus 'intergenic'. Genic variants name the gene (RefSeq v1.1); use genes_in_region for the genes near intergenic ones.
| Argument | Type | Description |
|---|---|---|
| limit | integer | |
| region* | string | |
| source | string | |
| consequence | any |
{
"type": "object",
"title": "wheat_variants_in_regionArguments",
"required": [
"region"
],
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"region": {
"type": "string",
"title": "Region"
},
"source": {
"type": "string",
"title": "Source",
"default": "all"
},
"consequence": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Consequence",
"default": null
}
}
}We read every tool's name, description and inputs the way the model will, looking for instructions hidden from you. A clean result means no warning signs, not a guarantee. Scanned Nov 14, 2026.
| any |
| genebank | any |
{
"type": "object",
"title": "genebank_phenotypesArguments",
"properties": {
"limit": {
"type": "integer",
"title": "Limit",
"default": 30
},
"order": {
"type": "string",
"title": "Order",
"default": "high"
},
"query": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Query",
"default": null
},
"trait": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Trait",
"default": null
},
"country": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Country",
"default": null
},
"dataset": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Dataset",
"default": null
},
"filters": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Filters",
"default": null
},
"genebank": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Genebank",
"default": null
}
}
}{
"type": "object",
"title": "search_literatureArguments",
"required": [
"query"
],
"properties": {
"gene": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Gene",
"default": null
},
"sort": {
"type": "string",
"title": "Sort",
"default": "relevance"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 10
},
"query": {
"type": "string",
"title": "Query"
},
"crop_only": {
"type": "boolean",
"title": "Crop Only",
"default": true
},
"from_year": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"title": "From Year",
"default": null
},
"full_text": {
"type": "boolean",
"title": "Full Text",
"default": false
},
"open_access_only": {
"type": "boolean",
"title": "Open Access Only",
"default": false
}
}
}{
"type": "object",
"title": "snp_haplotype_carriersArguments",
"required": [
"line",
"chromosome",
"start",
"end"
],
"properties": {
"end": {
"type": "integer",
"title": "End"
},
"line": {
"type": "string",
"title": "Line"
},
"limit": {
"type": "integer",
"title": "Limit",
"default": 200
},
"start": {
"type": "integer",
"title": "Start"
},
"dataset": {
"type": "string",
"title": "Dataset",
"default": "wheat40k"
},
"min_maf": {
"type": "number",
"title": "Min Maf",
"default": 0.05
},
"chromosome": {
"type": "string",
"title": "Chromosome"
},
"min_called": {
"type": "number",
"title": "Min Called",
"default": 1
},
"max_mismatch": {
"type": "integer",
"title": "Max Mismatch",
"default": 0
}
}
}