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Detailed information for vg1222240997:

Variant ID: vg1222240997 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22240997
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTACTATGGCAGTTTGAAAATGCTATTTAAACAATGGTTTTAAATAAATCTACACATTTAAGACTCCTTTGAATCACAGAAATAAAGAAATGAAAAAAT[G/A]
GAGAAATAGGAGAAACATAGGATTTAGACAGGAATATAAGTGTAAAACAAAGGATTGTAAAACACAGGAAAAATATAGGAATGACCGTTTGATTGAGCCG

Reverse complement sequence

CGGCTCAATCAAACGGTCATTCCTATATTTTTCCTGTGTTTTACAATCCTTTGTTTTACACTTATATTCCTGTCTAAATCCTATGTTTCTCCTATTTCTC[C/T]
ATTTTTTCATTTCTTTATTTCTGTGATTCAAAGGAGTCTTAAATGTGTAGATTTATTTAAAACCATTGTTTAAATAGCATTTTCAAACTGCCATAGTACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.80%	28.20%	0.76%	29.22%	NA
All Indica	2759	12.60%	46.80%	1.30%	39.22%	NA
All Japonica	1512	83.60%	0.50%	0.00%	15.87%	NA
Aus	269	78.10%	4.50%	0.00%	17.47%	NA
Indica I	595	10.40%	68.60%	0.00%	21.01%	NA
Indica II	465	11.80%	50.30%	2.15%	35.70%	NA
Indica III	913	13.80%	29.90%	2.08%	54.22%	NA
Indica Intermediate	786	13.50%	48.00%	0.89%	37.66%	NA
Temperate Japonica	767	87.70%	0.40%	0.00%	11.86%	NA
Tropical Japonica	504	77.20%	0.80%	0.00%	22.02%	NA
Japonica Intermediate	241	83.80%	0.40%	0.00%	15.77%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	66.70%	21.10%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222240997	G -> DEL	N	N	silent_mutation	Average:84.468; most accessible tissue: Minghui63 panicle, score: 94.307	N	N	N	N
vg1222240997	G -> A	LOC_Os12g36320.1	downstream_gene_variant ; 1819.0bp to feature; MODIFIER	silent_mutation	Average:84.468; most accessible tissue: Minghui63 panicle, score: 94.307	N	N	N	N
vg1222240997	G -> A	LOC_Os12g36330.1	downstream_gene_variant ; 3767.0bp to feature; MODIFIER	silent_mutation	Average:84.468; most accessible tissue: Minghui63 panicle, score: 94.307	N	N	N	N
vg1222240997	G -> A	LOC_Os12g36320-LOC_Os12g36330	intergenic_region ; MODIFIER	silent_mutation	Average:84.468; most accessible tissue: Minghui63 panicle, score: 94.307	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg1222240997	G	A	0.0	0.0	0.0	0.0	-0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222240997	6.48E-06	3.73E-06	mr1160_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251