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Detailed information for vg0801087393:

Variant ID: vg0801087393 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1087393
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.07, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTACAATTTGACTTCAGCTATTTTTTTCTTTCTGACATATATGTATTTACTATATTTTTTATCCAGTGTTTGTTTCACCTTGCTCCAAAATTTATTCA[A/T]
TTTTACTAGCTCCAAAATTTGTTCCTCTTTCTCTTTCTCTTTCTCTCTCTATTAGTAGGAGTAGCTGCTAAGCTGTGCCTGTAATCCTGTACTATCAGTA

Reverse complement sequence

TACTGATAGTACAGGATTACAGGCACAGCTTAGCAGCTACTCCTACTAATAGAGAGAGAAAGAGAAAGAGAAAGAGGAACAAATTTTGGAGCTAGTAAAA[T/A]
TGAATAAATTTTGGAGCAAGGTGAAACAAACACTGGATAAAAAATATAGTAAATACATATATGTCAGAAAGAAAAAAATAGCTGAAGTCAAATTGTACTA

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	67.50%	32.40%	0.17%	0.00%	NA
All Indica	2759	48.80%	51.10%	0.14%	0.00%	NA
All Japonica	1512	95.50%	4.40%	0.13%	0.00%	NA
Aus	269	90.30%	9.70%	0.00%	0.00%	NA
Indica I	595	34.60%	65.40%	0.00%	0.00%	NA
Indica II	465	14.40%	85.40%	0.22%	0.00%	NA
Indica III	913	76.10%	23.80%	0.11%	0.00%	NA
Indica Intermediate	786	48.10%	51.70%	0.25%	0.00%	NA
Temperate Japonica	767	92.40%	7.40%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.50%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	74.40%	23.30%	2.22%	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
vg0801087393	A -> T	LOC_Os08g02610.1	downstream_gene_variant ; 4833.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02630.1	downstream_gene_variant ; 2342.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02640.4	downstream_gene_variant ; 3759.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02640.5	downstream_gene_variant ; 3760.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02640.2	downstream_gene_variant ; 3761.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02640.3	downstream_gene_variant ; 3761.0bp to feature; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0801087393	A -> T	LOC_Os08g02610-LOC_Os08g02630	intergenic_region ; MODIFIER	silent_mutation	Average:88.137; most accessible tissue: Zhenshan97 panicle, score: 93.657	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)
vg0801087393	A	T	-0.01	0.0	0.0	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801087393	NA	9.59E-06	mr1277	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
vg0801087393	NA	3.54E-12	mr1352	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
vg0801087393	NA	2.04E-06	mr1352	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
vg0801087393	4.32E-06	NA	mr1397	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
vg0801087393	NA	2.15E-10	mr1739	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
vg0801087393	NA	1.36E-11	mr1751	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
vg0801087393	NA	1.64E-07	mr1811	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
vg0801087393	NA	1.26E-06	mr1850	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
vg0801087393	NA	4.07E-06	mr1255_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
vg0801087393	NA	1.31E-09	mr1739_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