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: intergenic_variant, intron_variant, upstream_gene_variant, downstream_gene_variant, 3_prime_UTR_variant, synonymous_variant, missense_variant, 5_prime_UTR_variant, grouped_splice_region, non_coding_transcript_exon_variant, grouped_start_stop

Consequence Types

Individual consequence types and their grouped variants:

• grouped_splice_region: splice_polypyrimidine_tract_variant, splice_region_variant, splice_donor_region_variant, splice_donor_variant, splice_donor_5th_base_variant, splice_acceptor_variant
• grouped_start_stop: stop_gained, stop_lost, start_lost

Filtered consequences (excluded from dataset): stop_retained_variant

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)