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Detailed information for vg0223558576:

Variant ID: vg0223558576 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23558576
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, A: 0.03, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCAGGTATACACACAGTAATGCCCAGATTTTTCTCACCAGCACACATCAGATCTAGTGACATACCAAACGAACAGTAAAAAAGACATCAATAAACTGC[T/A]
GCATACAGCAGCGGTTTCCACTCAGCGTGTACTTGCGCACTAGCGCGCTCATTGGGCCTCACAAGTACTACATGGAAACACGCGGCGTGCGTGCGTCCAT

Reverse complement sequence

ATGGACGCACGCACGCCGCGTGTTTCCATGTAGTACTTGTGAGGCCCAATGAGCGCGCTAGTGCGCAAGTACACGCTGAGTGGAAACCGCTGCTGTATGC[A/T]
GCAGTTTATTGATGTCTTTTTTACTGTTCGTTTGGTATGTCACTAGATCTGATGTGTGCTGGTGAGAAAAATCTGGGCATTACTGTGTGTATACCTGGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	34.70%	0.08%	0.72%	NA
All Indica	2759	57.60%	42.30%	0.07%	0.00%	NA
All Japonica	1512	76.90%	20.90%	0.00%	2.25%	NA
Aus	269	68.40%	31.60%	0.00%	0.00%	NA
Indica I	595	89.60%	10.40%	0.00%	0.00%	NA
Indica II	465	58.70%	41.10%	0.22%	0.00%	NA
Indica III	913	38.60%	61.30%	0.11%	0.00%	NA
Indica Intermediate	786	54.80%	45.20%	0.00%	0.00%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	39.30%	55.00%	0.00%	5.75%	NA
Japonica Intermediate	241	87.60%	10.40%	0.00%	2.07%	NA
VI/Aromatic	96	60.40%	38.50%	1.04%	0.00%	NA
Intermediate	90	63.30%	35.60%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0223558576	T -> A	LOC_Os02g38980.1	upstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38990.1	upstream_gene_variant ; 2548.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g39000.1	upstream_gene_variant ; 1164.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g39010.1	upstream_gene_variant ; 3700.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38980.4	upstream_gene_variant ; 4196.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38980.3	upstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38980.5	upstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38980.6	upstream_gene_variant ; 4194.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g39010.2	upstream_gene_variant ; 3700.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g39010.3	upstream_gene_variant ; 3700.0bp to feature; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> A	LOC_Os02g38990-LOC_Os02g39000	intergenic_region ; MODIFIER	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	N	N	N	N
vg0223558576	T -> DEL	N	N	silent_mutation	Average:94.255; most accessible tissue: Zhenshan97 panicle, score: 98.159	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)
vg0223558576	T	A	0.01	0.02	0.01	0.03	0.05	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223558576	NA	2.88E-06	mr1062_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0223558576	NA	1.02E-07	mr1149_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0223558576	7.56E-06	NA	mr1199_2	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
vg0223558576	NA	3.41E-09	mr1879_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251