Datasets:

plantcad
/

maize-allele-frequency

chrom large_stringclasses 5 values	pos int64 286k 308M	ref large_stringclasses 4 values	alt large_stringclasses 4 values	AC int64 4 2.3k	AN int64 2.45k 2.45k	AF float64 0 0.94	MAF float64 0 0.5	consequence large_stringclasses 11 values	original_consequence large_stringclasses 18 values
1	320,629	C	G	386	2,448	0.15768	0.15768	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	552,448	T	A	4	2,448	0.001634	0.001634	grouped_start_stop	stop_gained
1	1,023,179	T	A	12	2,448	0.004902	0.004902	grouped_start_stop	stop_gained
1	2,227,555	G	A	26	2,448	0.010621	0.010621	grouped_start_stop	stop_gained
1	2,290,521	C	T	22	2,448	0.008987	0.008987	missense_variant	missense_variant
1	2,291,600	T	C	150	2,448	0.061275	0.061275	synonymous_variant	synonymous_variant
1	2,291,802	T	A	6	2,448	0.002451	0.002451	grouped_splice_region	splice_region_variant
1	2,377,645	T	G	1,334	2,448	0.544935	0.455065	synonymous_variant	synonymous_variant
1	2,521,382	A	G	848	2,448	0.346405	0.346405	synonymous_variant	synonymous_variant
1	2,554,029	C	T	12	2,448	0.004902	0.004902	missense_variant	missense_variant
1	2,770,012	G	C	2,092	2,448	0.854575	0.145425	3_prime_UTR_variant	3_prime_UTR_variant
1	2,817,507	T	C	558	2,448	0.227941	0.227941	synonymous_variant	synonymous_variant
1	2,821,208	G	A	4	2,448	0.001634	0.001634	upstream_gene_variant	upstream_gene_variant
1	2,877,571	T	C	318	2,448	0.129902	0.129902	intron_variant	intron_variant
1	2,887,597	G	C	4	2,448	0.001634	0.001634	missense_variant	missense_variant
1	3,028,396	T	A	182	2,448	0.074346	0.074346	grouped_start_stop	stop_gained
1	3,043,104	A	C	524	2,448	0.214052	0.214052	grouped_start_stop	start_lost
1	3,094,912	C	G	4	2,448	0.001634	0.001634	upstream_gene_variant	upstream_gene_variant
1	3,099,452	T	C	108	2,448	0.044118	0.044118	intron_variant	intron_variant
1	3,113,048	C	T	664	2,448	0.271242	0.271242	grouped_splice_region	splice_region_variant
1	3,121,083	C	T	50	2,448	0.020425	0.020425	synonymous_variant	synonymous_variant
1	3,122,175	G	A	20	2,448	0.00817	0.00817	synonymous_variant	synonymous_variant
1	3,156,938	C	T	520	2,448	0.212418	0.212418	intergenic_variant	intergenic_variant
1	3,164,350	C	A	58	2,448	0.023693	0.023693	missense_variant	missense_variant
1	3,221,185	G	T	4	2,448	0.001634	0.001634	missense_variant	missense_variant
1	3,278,502	G	C	18	2,448	0.007353	0.007353	missense_variant	missense_variant
1	3,278,832	A	G	396	2,448	0.161765	0.161765	3_prime_UTR_variant	3_prime_UTR_variant
1	3,283,387	A	C	2,124	2,448	0.867647	0.132353	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	3,284,239	G	A	80	2,448	0.03268	0.03268	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	3,284,972	A	G	12	2,448	0.004902	0.004902	intron_variant	intron_variant
1	3,365,979	G	C	8	2,448	0.003268	0.003268	downstream_gene_variant	downstream_gene_variant
1	3,371,472	C	T	668	2,448	0.272876	0.272876	3_prime_UTR_variant	3_prime_UTR_variant
1	3,371,714	G	T	40	2,448	0.01634	0.01634	3_prime_UTR_variant	3_prime_UTR_variant
1	3,374,678	A	G	1,356	2,448	0.553922	0.446078	grouped_splice_region	splice_region_variant
1	3,438,142	T	G	2,002	2,448	0.81781	0.18219	upstream_gene_variant	upstream_gene_variant
1	3,442,863	G	A	536	2,448	0.218954	0.218954	grouped_splice_region	splice_donor_region_variant
1	3,652,383	C	T	434	2,448	0.177288	0.177288	upstream_gene_variant	upstream_gene_variant
1	3,735,851	A	G	386	2,448	0.15768	0.15768	downstream_gene_variant	downstream_gene_variant
1	3,764,387	T	C	98	2,448	0.040033	0.040033	intron_variant	intron_variant
1	3,796,916	A	T	506	2,448	0.206699	0.206699	grouped_start_stop	stop_gained
1	3,837,114	A	C	852	2,448	0.348039	0.348039	grouped_splice_region	splice_polypyrimidine_tract_variant
1	3,838,446	C	A	268	2,448	0.109477	0.109477	grouped_start_stop	stop_gained
1	3,959,665	A	G	1,050	2,448	0.428922	0.428922	5_prime_UTR_variant	5_prime_UTR_variant
1	3,964,956	C	T	22	2,448	0.008987	0.008987	downstream_gene_variant	downstream_gene_variant
1	4,094,107	A	G	796	2,448	0.325163	0.325163	synonymous_variant	synonymous_variant
1	4,102,988	G	C	922	2,448	0.376634	0.376634	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	4,104,354	G	A	68	2,448	0.027778	0.027778	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	4,111,251	G	A	4	2,448	0.001634	0.001634	downstream_gene_variant	downstream_gene_variant
1	4,235,851	G	A	12	2,448	0.004902	0.004902	intron_variant	intron_variant
1	4,291,172	G	A	4	2,448	0.001634	0.001634	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	4,293,886	G	A	114	2,448	0.046569	0.046569	5_prime_UTR_variant	5_prime_UTR_variant
1	4,302,360	C	G	62	2,448	0.025327	0.025327	intron_variant	intron_variant
1	4,304,611	C	T	382	2,448	0.156046	0.156046	3_prime_UTR_variant	3_prime_UTR_variant
1	4,355,554	G	T	164	2,448	0.066993	0.066993	intron_variant	intron_variant
1	4,359,461	C	T	136	2,448	0.055556	0.055556	missense_variant	missense_variant
1	4,371,159	C	G	6	2,448	0.002451	0.002451	grouped_splice_region	splice_polypyrimidine_tract_variant
1	4,372,937	G	A	126	2,448	0.051471	0.051471	grouped_start_stop	stop_gained
1	4,452,885	T	A	142	2,448	0.058007	0.058007	upstream_gene_variant	upstream_gene_variant
1	4,494,526	C	T	782	2,448	0.319444	0.319444	intergenic_variant	intergenic_variant
1	4,612,920	G	A	26	2,448	0.010621	0.010621	upstream_gene_variant	upstream_gene_variant
1	4,612,969	C	G	4	2,448	0.001634	0.001634	upstream_gene_variant	upstream_gene_variant
1	4,697,956	C	T	12	2,448	0.004902	0.004902	grouped_start_stop	stop_gained
1	4,793,772	C	A	68	2,448	0.027778	0.027778	grouped_start_stop	stop_gained
1	4,871,594	G	A	6	2,448	0.002451	0.002451	intergenic_variant	intergenic_variant
1	5,049,066	G	A	6	2,448	0.002451	0.002451	grouped_splice_region	splice_region_variant
1	5,051,110	G	A	30	2,448	0.012255	0.012255	grouped_start_stop	stop_gained
1	5,055,571	A	C	834	2,448	0.340686	0.340686	3_prime_UTR_variant	3_prime_UTR_variant
1	5,060,275	A	G	354	2,448	0.144608	0.144608	synonymous_variant	synonymous_variant
1	5,061,540	A	G	776	2,448	0.316993	0.316993	synonymous_variant	synonymous_variant
1	5,069,690	C	T	208	2,448	0.084967	0.084967	3_prime_UTR_variant	3_prime_UTR_variant
1	5,071,028	T	C	1,508	2,448	0.616013	0.383987	downstream_gene_variant	downstream_gene_variant
1	5,076,596	G	C	824	2,448	0.336601	0.336601	5_prime_UTR_variant	5_prime_UTR_variant
1	5,080,521	C	G	588	2,448	0.240196	0.240196	intron_variant	intron_variant
1	5,116,061	T	C	26	2,448	0.010621	0.010621	downstream_gene_variant	downstream_gene_variant
1	5,116,187	G	C	124	2,448	0.050654	0.050654	downstream_gene_variant	downstream_gene_variant
1	5,261,845	T	G	4	2,448	0.001634	0.001634	intergenic_variant	intergenic_variant
1	5,384,155	T	C	4	2,448	0.001634	0.001634	upstream_gene_variant	upstream_gene_variant
1	5,419,964	G	C	6	2,448	0.002451	0.002451	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	5,423,259	T	C	72	2,448	0.029412	0.029412	upstream_gene_variant	upstream_gene_variant
1	5,424,016	T	C	452	2,448	0.184641	0.184641	5_prime_UTR_variant	5_prime_UTR_variant
1	5,424,534	G	T	232	2,448	0.094771	0.094771	intron_variant	intron_variant
1	5,476,331	A	G	262	2,448	0.107026	0.107026	missense_variant	missense_variant
1	5,556,546	C	T	8	2,448	0.003268	0.003268	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	5,652,796	A	G	1,438	2,448	0.587418	0.412582	3_prime_UTR_variant	3_prime_UTR_variant
1	5,659,964	G	T	12	2,448	0.004902	0.004902	missense_variant	missense_variant
1	5,759,097	T	G	8	2,448	0.003268	0.003268	intron_variant	intron_variant
1	5,764,850	G	A	136	2,448	0.055556	0.055556	intron_variant	intron_variant
1	5,766,064	C	T	8	2,448	0.003268	0.003268	3_prime_UTR_variant	3_prime_UTR_variant
1	5,766,970	G	A	758	2,448	0.309641	0.309641	downstream_gene_variant	downstream_gene_variant
1	5,778,739	C	G	36	2,448	0.014706	0.014706	upstream_gene_variant	upstream_gene_variant
1	5,836,390	C	A	8	2,448	0.003268	0.003268	upstream_gene_variant	upstream_gene_variant
1	5,838,955	C	T	6	2,448	0.002451	0.002451	synonymous_variant	synonymous_variant
1	5,847,126	C	T	14	2,448	0.005719	0.005719	3_prime_UTR_variant	3_prime_UTR_variant
1	5,857,615	G	A	118	2,448	0.048203	0.048203	grouped_splice_region	splice_region_variant
1	5,899,843	C	A	4	2,448	0.001634	0.001634	synonymous_variant	synonymous_variant
1	6,022,162	A	G	126	2,448	0.051471	0.051471	grouped_splice_region	splice_donor_region_variant
1	6,190,057	A	G	34	2,448	0.013889	0.013889	downstream_gene_variant	downstream_gene_variant
1	6,190,784	G	A	64	2,448	0.026144	0.026144	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	6,190,913	T	A	4	2,448	0.001634	0.001634	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant
1	6,190,916	C	G	4	2,448	0.001634	0.001634	non_coding_transcript_exon_variant	non_coding_transcript_exon_variant

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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)

Downloads last month: 140

Size of downloaded dataset files:

68 MB

Size of the auto-converted Parquet files:

68 MB

Number of rows:

10,038,154