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Detailed information for vg0200334269:

Variant ID: vg0200334269 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 334269
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGAGAAACTTCAAATTTGACGTTTCTCTCTCCCCGGATGGAGGATAGCTAAATTTGGATGCTAGGATGGAGTATCTGCTGGAGCTCATTTTTCTTCTC[C/T]
CAACCTCTATTTTGTGGATAGAGGACTAGATGGAGTATCTGCTGGGGATGCTCTAATATATACTATATGCACTAATAACTCCAATATAGGAAAACACGTT

Reverse complement sequence

AACGTGTTTTCCTATATTGGAGTTATTAGTGCATATAGTATATATTAGAGCATCCCCAGCAGATACTCCATCTAGTCCTCTATCCACAAAATAGAGGTTG[G/A]
GAGAAGAAAAATGAGCTCCAGCAGATACTCCATCCTAGCATCCAAATTTAGCTATCCTCCATCCGGGGAGAGAGAAACGTCAAATTTGAAGTTTCTCTCT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.20%	9.60%	0.25%	0.00%	NA
All Indica	2759	87.00%	12.80%	0.22%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	63.90%	33.80%	2.23%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	89.20%	10.80%	0.00%	0.00%	NA
Indica III	913	81.90%	17.70%	0.33%	0.00%	NA
Indica Intermediate	786	82.40%	17.20%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0200334269	C -> T	LOC_Os02g01580.1	upstream_gene_variant ; 3813.0bp to feature; MODIFIER	silent_mutation	Average:81.037; most accessible tissue: Minghui63 flower, score: 94.603	N	N	N	N
vg0200334269	C -> T	LOC_Os02g01580-LOC_Os02g01590	intergenic_region ; MODIFIER	silent_mutation	Average:81.037; most accessible tissue: Minghui63 flower, score: 94.603	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)
vg0200334269	C	T	0.04	0.03	0.07	0.03	0.06	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200334269	NA	5.73E-06	mr1048	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
vg0200334269	NA	4.14E-07	mr1190	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
vg0200334269	NA	3.46E-07	mr1286	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
vg0200334269	NA	7.32E-06	mr1287	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
vg0200334269	NA	7.72E-06	mr1393	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
vg0200334269	NA	8.46E-07	mr1417	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
vg0200334269	NA	3.85E-06	mr1445	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
vg0200334269	NA	2.23E-06	mr1485	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
vg0200334269	NA	9.89E-07	mr1574	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
vg0200334269	4.95E-06	4.95E-06	mr1643	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
vg0200334269	NA	1.25E-07	mr1665	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
vg0200334269	NA	8.69E-08	mr1774	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
vg0200334269	NA	3.31E-06	mr1777	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
vg0200334269	NA	5.69E-06	mr1988	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