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Detailed information for vg0808431667:

Variant ID: vg0808431667 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8431667
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: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGTTGATTTTGACCAGTATATATGAATTGATCCTGCAGGTAAAAGCAGCTGAAGATGCTAAAGCAATCTTTTCTGATCTAAGAAAGAAAGGGATATCT[G/A]
TTATTTGGAGTTGGAGGTTACTGTTGGGGTGGTGAGTGATATTAATCAACATAAAGAAGAAGCACATTAATTTGTGCATTTATAATTATACTACTACATC

Reverse complement sequence

GATGTAGTAGTATAATTATAAATGCACAAATTAATGTGCTTCTTCTTTATGTTGATTAATATCACTCACCACCCCAACAGTAACCTCCAACTCCAAATAA[C/T]
AGATATCCCTTTCTTTCTTAGATCAGAAAAGATTGCTTTAGCATCTTCAGCTGCTTTTACCTGCAGGATCAATTCATATATACTGGTCAAAATCAACTTA

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	20.00%	16.80%	14.68%	48.58%	NA
All Indica	2759	3.60%	24.70%	15.04%	56.69%	NA
All Japonica	1512	53.50%	0.30%	11.24%	34.99%	NA
Aus	269	2.60%	33.80%	11.52%	52.04%	NA
Indica I	595	4.40%	19.30%	8.24%	68.07%	NA
Indica II	465	3.70%	5.60%	4.95%	85.81%	NA
Indica III	913	2.10%	39.30%	27.82%	30.78%	NA
Indica Intermediate	786	4.60%	23.20%	11.32%	60.94%	NA
Temperate Japonica	767	72.20%	0.30%	1.30%	26.21%	NA
Tropical Japonica	504	18.80%	0.40%	21.43%	59.33%	NA
Japonica Intermediate	241	66.40%	0.00%	21.58%	12.03%	NA
VI/Aromatic	96	10.40%	6.20%	66.67%	16.67%	NA
Intermediate	90	21.10%	11.10%	15.56%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808431667	G -> A	LOC_Os08g14090.1	missense_variant ; p.Val71Ile; MODERATE	nonsynonymous_codon ; V71I	Average:53.772; most accessible tissue: Zhenshan97 young leaf, score: 65.804	unknown	unknown	TOLERATED	0.60
vg0808431667	G -> DEL	LOC_Os08g14090.1	N	frameshift_variant	Average:53.772; most accessible tissue: Zhenshan97 young leaf, score: 65.804	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808431667	NA	5.88E-07	mr1114	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
vg0808431667	NA	5.41E-06	mr1115	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
vg0808431667	NA	7.42E-06	mr1116	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
vg0808431667	NA	9.44E-06	mr1168	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
vg0808431667	NA	1.88E-06	mr1180	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
vg0808431667	1.90E-06	NA	mr1233	Ind_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
vg0808431667	NA	4.47E-06	mr1383	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
vg0808431667	NA	1.13E-06	mr1510	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
vg0808431667	NA	4.86E-06	mr1844	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