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Detailed information for vg0818081691:

Variant ID: vg0818081691 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18081691
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CCCTTTGCAGTGCCGTGGTGGTACTTCGGGGCATGGCAACATGTGTGGAATCGTGTCTTGTAGGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTC[G/A]
AATAGCCGTGCCCGCGGTTATGGGCGGGTTGAGCAATGTTTTTTTGATTAGTCTCACAACTCTCACAAATAATTATTGATGCAATAACTGGTAATAATTT

Reverse complement sequence

AAATTATTACCAGTTATTGCATCAATAATTATTTGTGAGAGTTGTGAGACTAATCAAAAAAACATTGCTCAACCCGCCCATAACCGCGGGCACGGCTATT[C/T]
GAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACCTACAAGACACGATTCCACACATGTTGCCATGCCCCGAAGTACCACCACGGCACTGCAAAGGG

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	56.60%	26.00%	17.41%	0.00%	NA
All Indica	2759	41.80%	30.20%	28.05%	0.00%	NA
All Japonica	1512	73.70%	24.20%	2.12%	0.00%	NA
Aus	269	98.10%	1.50%	0.37%	0.00%	NA
Indica I	595	47.90%	24.40%	27.73%	0.00%	NA
Indica II	465	20.20%	35.10%	44.73%	0.00%	NA
Indica III	913	44.10%	34.50%	21.36%	0.00%	NA
Indica Intermediate	786	47.20%	26.60%	26.21%	0.00%	NA
Temperate Japonica	767	97.70%	1.80%	0.52%	0.00%	NA
Tropical Japonica	504	37.30%	58.70%	3.97%	0.00%	NA
Japonica Intermediate	241	73.40%	23.20%	3.32%	0.00%	NA
VI/Aromatic	96	90.60%	7.30%	2.08%	0.00%	NA
Intermediate	90	62.20%	22.20%	15.56%	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
vg0818081691	G -> A	LOC_Os08g29490.1	upstream_gene_variant ; 3311.0bp to feature; MODIFIER	silent_mutation	Average:59.466; most accessible tissue: Zhenshan97 flag leaf, score: 82.351	N	N	N	N
vg0818081691	G -> A	LOC_Os08g29490-LOC_Os08g29500	intergenic_region ; MODIFIER	silent_mutation	Average:59.466; most accessible tissue: Zhenshan97 flag leaf, score: 82.351	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818081691	2.71E-06	2.70E-06	mr1572	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
vg0818081691	NA	3.33E-06	mr1544_2	Jap_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
vg0818081691	NA	2.76E-09	mr1952_2	Jap_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