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Detailed information for vg0232914706:

Variant ID: vg0232914706 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32914706
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TATTAGGGCTTAAGATGTACGGGCAATACGACAATGAACAATTGATTTTTAACTGGAAAAATTGAAAGTTTGGTTGAAATTGGAACGATGTGATGGAAAA[T/A]
TTGAAAGTTTGTGTGTAGCCGTGTAAGAAAGTTTTGATGTGATGGAAAAATTGAAAGTTTGAAGAAAAAATTTGGAACTAAACTCGGCCTGACATGTGAT

Reverse complement sequence

ATCACATGTCAGGCCGAGTTTAGTTCCAAATTTTTTCTTCAAACTTTCAATTTTTCCATCACATCAAAACTTTCTTACACGGCTACACACAAACTTTCAA[A/T]
TTTTCCATCACATCGTTCCAATTTCAACCAAACTTTCAATTTTTCCAGTTAAAAATCAATTGTTCATTGTCGTATTGCCCGTACATCTTAAGCCCTAATA

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	75.60%	22.40%	1.99%	0.00%	NA
All Indica	2759	98.70%	0.90%	0.33%	0.00%	NA
All Japonica	1512	29.60%	65.00%	5.36%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	97.60%	2.20%	0.22%	0.00%	NA
Indica III	913	98.90%	0.90%	0.22%	0.00%	NA
Indica Intermediate	786	98.50%	1.00%	0.51%	0.00%	NA
Temperate Japonica	767	36.20%	54.10%	9.65%	0.00%	NA
Tropical Japonica	504	4.20%	95.80%	0.00%	0.00%	NA
Japonica Intermediate	241	61.80%	35.30%	2.90%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	56.70%	38.90%	4.44%	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
vg0232914706	T -> A	LOC_Os02g53740.2	downstream_gene_variant ; 934.0bp to feature; MODIFIER	silent_mutation	Average:72.855; most accessible tissue: Zhenshan97 flag leaf, score: 88.918	N	N	N	N
vg0232914706	T -> A	LOC_Os02g53750.1	downstream_gene_variant ; 602.0bp to feature; MODIFIER	silent_mutation	Average:72.855; most accessible tissue: Zhenshan97 flag leaf, score: 88.918	N	N	N	N
vg0232914706	T -> A	LOC_Os02g53740.3	downstream_gene_variant ; 934.0bp to feature; MODIFIER	silent_mutation	Average:72.855; most accessible tissue: Zhenshan97 flag leaf, score: 88.918	N	N	N	N
vg0232914706	T -> A	LOC_Os02g53750.2	downstream_gene_variant ; 602.0bp to feature; MODIFIER	silent_mutation	Average:72.855; most accessible tissue: Zhenshan97 flag leaf, score: 88.918	N	N	N	N
vg0232914706	T -> A	LOC_Os02g53740-LOC_Os02g53750	intergenic_region ; MODIFIER	silent_mutation	Average:72.855; most accessible tissue: Zhenshan97 flag leaf, score: 88.918	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)
vg0232914706	T	A	0.02	0.01	0.01	0.0	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232914706	NA	1.02E-08	Yield	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0232914706	NA	2.77E-14	mr1062	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
vg0232914706	NA	9.52E-09	mr1585	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
vg0232914706	NA	2.06E-11	mr1623	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
vg0232914706	NA	1.30E-11	mr1626	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
vg0232914706	NA	4.97E-11	mr1905	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
vg0232914706	NA	2.64E-19	mr1062_2	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
vg0232914706	NA	1.72E-09	mr1354_2	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
vg0232914706	NA	9.74E-08	mr1585_2	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
vg0232914706	NA	6.02E-07	mr1623_2	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
vg0232914706	NA	2.90E-11	mr1705_2	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
vg0232914706	NA	5.51E-11	mr1761_2	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
vg0232914706	NA	2.18E-08	mr1765_2	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