plantcad/maize-allele-frequency

Maize Allele Frequency Dataset

Source data described in PlantCaduceus paper. Raw data available at plantcad/maize-allele-frequency-raw-data.

Splits

• —validation: Chromosomes 1, 3, 5, 7, 9
• —test: Chromosomes 2, 4, 6, 8, 10

Configurations

full

Complete dataset with all variants.

Subsampled Configurations

Subsampled datasets (excluding repeats) with max N variants, filtered by consequence type:

• —{max_n}_all_consequences: Balanced sample across all consequence types (~N/11 per consequence)
• —{max_n}_{consequence}: Up to N variants of specific consequence type

Available sample sizes: 10k, 20k

Available consequence types: intergenicvariant, intronvariant, upstreamgenevariant, downstreamgenevariant, 3primeUTRvariant, synonymousvariant, missensevariant, 5primeUTRvariant, groupedspliceregion, noncodingtranscriptexonvariant, groupedstartstop

Consequence Types

Individual consequence types and their grouped variants:

• —grouped_splice_region: splicepolypyrimidinetractvariant, spliceregionvariant, splicedonorregionvariant, splicedonorvariant, splicedonor5thbasevariant, spliceacceptorvariant
• —grouped_start_stop: stopgained, stoplost, start_lost

Filtered consequences (excluded from dataset): stopretainedvariant

Data Schema

• —chrom: Chromosome
• —pos: Position
• —ref: Reference allele
• —alt: Alternate allele
• —AC: Allele count
• —AN: Allele number
• —AF: Allele frequency
• —MAF: Minor allele frequency
• —consequence: Consequence type (after grouping)
• —original_consequence: Original Ensembl VEP consequence (before grouping)