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Detailed information for vg0813418895:

Variant ID: vg0813418895 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13418895
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTTCACCCAAGCAGACCCCTCCAACTCCTTCTGCCCCAACTCATTTTTCAAGAGTAAGCAGCTCTCTTTGATCCTTTTTGTAATCACTTCATTTTTTC[G/A,T]
GCCGATTACTCACAGACTTTATAGTTGCAGAAGAAGAAAATTGCTGTGAAAAAGAAACCAGCAGCAACAATTCTCAAACCGGCTCCACCAGTAAGTTATT

Reverse complement sequence

AATAACTTACTGGTGGAGCCGGTTTGAGAATTGTTGCTGCTGGTTTCTTTTTCACAGCAATTTTCTTCTTCTGCAACTATAAAGTCTGTGAGTAATCGGC[C/T,A]
GAAAAAATGAAGTGATTACAAAAAGGATCAAAGAGAGCTGCTTACTCTTGAAAAATGAGTTGGGGCAGAAGGAGTTGGAGGGGTCTGCTTGGGTGAAGCC

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	50.10%	43.00%	6.31%	0.28%	T: 0.32%
All Indica	2759	21.90%	68.90%	8.59%	0.07%	T: 0.51%
All Japonica	1512	95.80%	1.50%	1.98%	0.66%	NA
Aus	269	59.10%	32.30%	8.55%	0.00%	NA
Indica I	595	11.90%	81.30%	6.72%	0.00%	NA
Indica II	465	22.60%	69.00%	7.74%	0.00%	T: 0.65%
Indica III	913	24.60%	64.60%	9.75%	0.11%	T: 0.88%
Indica Intermediate	786	25.80%	64.50%	9.16%	0.13%	T: 0.38%
Temperate Japonica	767	97.80%	1.80%	0.39%	0.00%	NA
Tropical Japonica	504	92.90%	0.60%	4.56%	1.98%	NA
Japonica Intermediate	241	95.90%	2.50%	1.66%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	66.70%	22.20%	8.89%	1.11%	T: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813418895	G -> T	LOC_Os08g22270.1	downstream_gene_variant ; 1695.0bp to feature; MODIFIER	silent_mutation	Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg0813418895	G -> T	LOC_Os08g22260.1	intron_variant ; MODIFIER	silent_mutation	Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg0813418895	G -> A	LOC_Os08g22270.1	downstream_gene_variant ; 1695.0bp to feature; MODIFIER	silent_mutation	Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg0813418895	G -> A	LOC_Os08g22260.1	intron_variant ; MODIFIER	silent_mutation	Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N
vg0813418895	G -> DEL	N	N	silent_mutation	Average:33.119; most accessible tissue: Zhenshan97 flag leaf, score: 46.427	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813418895	1.50E-06	3.09E-06	mr1582	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