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Detailed information for vg1117508504:

Variant ID: vg1117508504 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17508504
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGTGCCTAGCCCTGTACATACATGTCCAGATGTTTTGGCTGTCATCTCTTCTGCTAACTCTCCCTTTTGACTTTACTTACTTGCTGAGTTCCTCATC[A/T]
GTTCCCTTCCTCTCTTTCCAAGCTTGCTTCCATCGTCGACATCTCCTCCTTGATCCGAGTAGCTCGTGATGGCCGGACTACTTGCCTCTCTGGCCATAAG

Reverse complement sequence

CTTATGGCCAGAGAGGCAAGTAGTCCGGCCATCACGAGCTACTCGGATCAAGGAGGAGATGTCGACGATGGAAGCAAGCTTGGAAAGAGAGGAAGGGAAC[T/A]
GATGAGGAACTCAGCAAGTAAGTAAAGTCAAAAGGGAGAGTTAGCAGAAGAGATGACAGCCAAAACATCTGGACATGTATGTACAGGGCTAGGCACATTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.10%	29.50%	0.06%	5.35%	NA
All Indica	2759	43.20%	48.70%	0.11%	7.90%	NA
All Japonica	1512	98.80%	0.90%	0.00%	0.33%	NA
Aus	269	90.70%	7.80%	0.00%	1.49%	NA
Indica I	595	34.10%	62.90%	0.17%	2.86%	NA
Indica II	465	35.90%	46.50%	0.22%	17.42%	NA
Indica III	913	50.40%	41.40%	0.00%	8.21%	NA
Indica Intermediate	786	46.20%	48.00%	0.13%	5.73%	NA
Temperate Japonica	767	98.70%	0.90%	0.00%	0.39%	NA
Tropical Japonica	504	99.00%	0.80%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.80%	0.00%	0.41%	NA
VI/Aromatic	96	80.20%	0.00%	0.00%	19.79%	NA
Intermediate	90	75.60%	16.70%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117508504	A -> T	LOC_Os11g30100.1	upstream_gene_variant ; 1431.0bp to feature; MODIFIER	silent_mutation	Average:83.869; most accessible tissue: Zhenshan97 root, score: 98.728	N	N	N	N
vg1117508504	A -> T	LOC_Os11g30110.1	upstream_gene_variant ; 69.0bp to feature; MODIFIER	silent_mutation	Average:83.869; most accessible tissue: Zhenshan97 root, score: 98.728	N	N	N	N
vg1117508504	A -> T	LOC_Os11g30090.1	downstream_gene_variant ; 3315.0bp to feature; MODIFIER	silent_mutation	Average:83.869; most accessible tissue: Zhenshan97 root, score: 98.728	N	N	N	N
vg1117508504	A -> T	LOC_Os11g30100-LOC_Os11g30110	intergenic_region ; MODIFIER	silent_mutation	Average:83.869; most accessible tissue: Zhenshan97 root, score: 98.728	N	N	N	N
vg1117508504	A -> DEL	N	N	silent_mutation	Average:83.869; most accessible tissue: Zhenshan97 root, score: 98.728	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)
vg1117508504	A	T	0.07	0.06	0.03	0.02	0.05	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117508504	NA	2.13E-10	mr1151	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
vg1117508504	NA	1.50E-08	mr1170	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
vg1117508504	NA	8.34E-07	mr1450	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
vg1117508504	NA	5.80E-06	mr1534	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
vg1117508504	NA	2.90E-06	mr1921	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
vg1117508504	NA	1.49E-06	mr1968	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
vg1117508504	NA	1.69E-11	mr1970	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
vg1117508504	NA	2.73E-09	mr1973	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
vg1117508504	NA	1.89E-06	mr1170_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
vg1117508504	NA	4.62E-07	mr1970_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
vg1117508504	NA	2.19E-07	mr1973_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