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Detailed information for vg1126339132:

Variant ID: vg1126339132 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26339132
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.09, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TACGGTACACTATACTGCAAGTATAAACAATCTAATGATATAGATTCATCTGATCTTTCCTCTAGATTAGTTTACAATATAAATTGAAAAGGGTAAATTT[A/G]
TCTTTCCATCTTTTTGCGCGTTTCCTTCTTCGGTCAGATCTGGCCCAAGAGAAATCTGCTCAAGAGAATTCCGGTCGCTTTCTTTCATCCCATGCGCTAC

Reverse complement sequence

GTAGCGCATGGGATGAAAGAAAGCGACCGGAATTCTCTTGAGCAGATTTCTCTTGGGCCAGATCTGACCGAAGAAGGAAACGCGCAAAAAGATGGAAAGA[T/C]
AAATTTACCCTTTTCAATTTATATTGTAAACTAATCTAGAGGAAAGATCAGATGAATCTATATCATTAGATTGTTTATACTTGCAGTATAGTGTACCGTA

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	77.80%	20.50%	0.57%	1.10%	NA
All Indica	2759	79.60%	19.60%	0.07%	0.76%	NA
All Japonica	1512	75.40%	24.30%	0.33%	0.00%	NA
Aus	269	67.30%	14.50%	6.69%	11.52%	NA
Indica I	595	96.00%	2.50%	0.00%	1.51%	NA
Indica II	465	87.30%	12.70%	0.00%	0.00%	NA
Indica III	913	66.90%	32.50%	0.11%	0.44%	NA
Indica Intermediate	786	77.20%	21.60%	0.13%	1.02%	NA
Temperate Japonica	767	67.50%	32.20%	0.26%	0.00%	NA
Tropical Japonica	504	92.30%	7.70%	0.00%	0.00%	NA
Japonica Intermediate	241	65.10%	33.60%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	75.60%	23.30%	1.11%	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
vg1126339132	A -> DEL	N	N	silent_mutation	Average:35.846; most accessible tissue: Zhenshan97 young leaf, score: 53.969	N	N	N	N
vg1126339132	A -> G	LOC_Os11g43650-LOC_Os11g43660	intergenic_region ; MODIFIER	silent_mutation	Average:35.846; most accessible tissue: Zhenshan97 young leaf, score: 53.969	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126339132	NA	9.84E-08	mr1662	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
vg1126339132	NA	2.73E-07	mr1045_2	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
vg1126339132	3.29E-06	4.45E-08	mr1158_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
vg1126339132	NA	8.63E-06	mr1206_2	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
vg1126339132	NA	8.64E-06	mr1763_2	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