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Detailed information for vg0818210018:

Variant ID: vg0818210018 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18210018
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.52, G: 0.48, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

AGATAATTTGGACTACACATTAATCATTCAAAGGCTAAAAAAAATTGAGGTAATGTGACTTAATGAGATAATAGAGAAATGATTAACTAAATGGGGACGA[A/G]
CTATGTATGTATATAAAATATTGTAGAAAATGATGAGTATATATTAAAATTTTATGTAAATGATGTGGGATGATGATTTAACATACTTAAATTTTAAAAC

Reverse complement sequence

GTTTTAAAATTTAAGTATGTTAAATCATCATCCCACATCATTTACATAAAATTTTAATATATACTCATCATTTTCTACAATATTTTATATACATACATAG[T/C]
TCGTCCCCATTTAGTTAATCATTTCTCTATTATCTCATTAAGTCACATTACCTCAATTTTTTTTAGCCTTTGAATGATTAATGTGTAGTCCAAATTATCT

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	64.10%	35.90%	0.04%	0.00%	NA
All Indica	2759	90.60%	9.40%	0.04%	0.00%	NA
All Japonica	1512	23.60%	76.30%	0.07%	0.00%	NA
Aus	269	11.50%	88.50%	0.00%	0.00%	NA
Indica I	595	86.40%	13.60%	0.00%	0.00%	NA
Indica II	465	90.80%	9.20%	0.00%	0.00%	NA
Indica III	913	97.50%	2.50%	0.00%	0.00%	NA
Indica Intermediate	786	85.60%	14.20%	0.13%	0.00%	NA
Temperate Japonica	767	14.10%	85.90%	0.00%	0.00%	NA
Tropical Japonica	504	34.10%	65.70%	0.20%	0.00%	NA
Japonica Intermediate	241	32.00%	68.00%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	61.10%	38.90%	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
vg0818210018	A -> G	LOC_Os08g29650-LOC_Os08g29660	intergenic_region ; MODIFIER	silent_mutation	Average:34.161; most accessible tissue: Callus, score: 57.794	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818210018	NA	2.71E-07	mr1021	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
vg0818210018	2.17E-07	2.17E-07	mr1207	Jap_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
vg0818210018	NA	8.91E-06	mr1477	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
vg0818210018	NA	2.62E-06	mr1522	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