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Detailed information for vg0210040759:

Variant ID: vg0210040759 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10040759
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, G: 0.09, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATTATTTCCAAGGCTCTGAAAATTCCACTAAAAATCCTGTTAATATATTGCAACATGGGGAACTCAAGAAAAATTCCACCACGCCATTTCCGATTAT[T/G]
AATTGCATTGATTAATTAGGGATTCAACTCTAGGTTAATTAAACAATTTCTTCGAGCAATTTATTTAACCAATTTTTTTAGCAAGAAAAGGGGGAAACTT

Reverse complement sequence

AAGTTTCCCCCTTTTCTTGCTAAAAAAATTGGTTAAATAAATTGCTCGAAGAAATTGTTTAATTAACCTAGAGTTGAATCCCTAATTAATCAATGCAATT[A/C]
ATAATCGGAAATGGCGTGGTGGAATTTTTCTTGAGTTCCCCATGTTGCAATATATTAACAGGATTTTTAGTGGAATTTTCAGAGCCTTGGAAATAATTTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.00%	40.50%	0.47%	18.11%	NA
All Indica	2759	44.80%	24.20%	0.72%	30.19%	NA
All Japonica	1512	32.50%	66.80%	0.13%	0.53%	NA
Aus	269	59.50%	40.50%	0.00%	0.00%	NA
Indica I	595	36.10%	21.20%	0.34%	42.35%	NA
Indica II	465	36.60%	22.20%	1.29%	40.00%	NA
Indica III	913	56.10%	32.20%	0.33%	11.39%	NA
Indica Intermediate	786	43.30%	18.60%	1.15%	37.02%	NA
Temperate Japonica	767	59.70%	39.40%	0.13%	0.78%	NA
Tropical Japonica	504	3.80%	96.00%	0.00%	0.20%	NA
Japonica Intermediate	241	6.20%	92.90%	0.41%	0.41%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	40.00%	43.30%	0.00%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210040759	T -> G	LOC_Os02g17440.1	upstream_gene_variant ; 1897.0bp to feature; MODIFIER	silent_mutation	Average:25.19; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0210040759	T -> G	LOC_Os02g17460.1	downstream_gene_variant ; 1719.0bp to feature; MODIFIER	silent_mutation	Average:25.19; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0210040759	T -> G	LOC_Os02g17450.1	intron_variant ; MODIFIER	silent_mutation	Average:25.19; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0210040759	T -> DEL	N	N	silent_mutation	Average:25.19; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210040759	NA	9.53E-06	mr1508	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
vg0210040759	1.39E-06	1.39E-06	mr1267_2	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