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Detailed information for vg0825781053:

Variant ID: vg0825781053 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25781053
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

AAATCTCGGCAGGACCCACCACGTACCATGTCCTATACGGAAACAACCTGCGGATATAGGAGGAGTTCTGGATAAGGAAAGACAACCAGAGTTCTATATG[G/A]
AAACGACAAGGACTACTCGGATTGTATCCATATTGGTTTCCCTAGTTCTACTTGGACAATGGGACATTTATGAGTATAAATACAAGACCCCCTAGGAGGA

Reverse complement sequence

TCCTCCTAGGGGGTCTTGTATTTATACTCATAAATGTCCCATTGTCCAAGTAGAACTAGGGAAACCAATATGGATACAATCCGAGTAGTCCTTGTCGTTT[C/T]
CATATAGAACTCTGGTTGTCTTTCCTTATCCAGAACTCCTCCTATATCCGCAGGTTGTTTCCGTATAGGACATGGTACGTGGTGGGTCCTGCCGAGATTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.30%	15.50%	0.13%	0.00%	NA
All Indica	2759	83.00%	16.90%	0.11%	0.00%	NA
All Japonica	1512	98.30%	1.60%	0.07%	0.00%	NA
Aus	269	23.80%	76.20%	0.00%	0.00%	NA
Indica I	595	84.90%	15.00%	0.17%	0.00%	NA
Indica II	465	93.30%	6.70%	0.00%	0.00%	NA
Indica III	913	81.60%	18.40%	0.00%	0.00%	NA
Indica Intermediate	786	77.20%	22.50%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	7.90%	0.41%	0.00%	NA
VI/Aromatic	96	74.00%	25.00%	1.04%	0.00%	NA
Intermediate	90	81.10%	17.80%	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
vg0825781053	G -> A	LOC_Os08g40740.1	upstream_gene_variant ; 1692.0bp to feature; MODIFIER	silent_mutation	Average:57.995; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0825781053	G -> A	LOC_Os08g40750.1	downstream_gene_variant ; 132.0bp to feature; MODIFIER	silent_mutation	Average:57.995; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0825781053	G -> A	LOC_Os08g40740-LOC_Os08g40750	intergenic_region ; MODIFIER	silent_mutation	Average:57.995; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825781053	NA	1.11E-06	mr1028	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
vg0825781053	NA	2.81E-07	mr1453	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