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Detailed information for vg1125216297:

Variant ID: vg1125216297 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25216297
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTGATGATAGAACATATAGAAAAACTATTTAATTGATCTGGGTATATCCAACACCGCTATGAATTTCATATTAGGAGTAATGTTTTGTGCTCTACCAT[A/G]
CCTGCTGTTATAAGTCATATGATGATGAGGTTAAATAGAATTGTCATACTAATTACTCCATCTGTTCTTGGCAGGTAAATCTGCAGACAACAGCTTGCAG

Reverse complement sequence

CTGCAAGCTGTTGTCTGCAGATTTACCTGCCAAGAACAGATGGAGTAATTAGTATGACAATTCTATTTAACCTCATCATCATATGACTTATAACAGCAGG[T/C]
ATGGTAGAGCACAAAACATTACTCCTAATATGAAATTCATAGCGGTGTTGGATATACCCAGATCAATTAAATAGTTTTTCTATATGTTCTATCATCACAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.20%	25.70%	0.11%	0.00%	NA
All Indica	2759	61.90%	38.00%	0.11%	0.00%	NA
All Japonica	1512	93.20%	6.70%	0.13%	0.00%	NA
Aus	269	82.90%	17.10%	0.00%	0.00%	NA
Indica I	595	70.30%	29.60%	0.17%	0.00%	NA
Indica II	465	61.90%	38.10%	0.00%	0.00%	NA
Indica III	913	60.60%	39.40%	0.00%	0.00%	NA
Indica Intermediate	786	57.00%	42.70%	0.25%	0.00%	NA
Temperate Japonica	767	97.50%	2.20%	0.26%	0.00%	NA
Tropical Japonica	504	87.30%	12.70%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg1125216297	A -> G	LOC_Os11g41920.1	upstream_gene_variant ; 2030.0bp to feature; MODIFIER	silent_mutation	Average:62.817; most accessible tissue: Callus, score: 89.558	N	N	N	N
vg1125216297	A -> G	LOC_Os11g41910.1	intron_variant ; MODIFIER	silent_mutation	Average:62.817; most accessible tissue: Callus, score: 89.558	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125216297	2.74E-08	NA	mr1191	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
vg1125216297	1.82E-08	1.43E-12	mr1191	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
vg1125216297	1.08E-07	NA	mr1644	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
vg1125216297	7.18E-08	4.89E-13	mr1644	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
vg1125216297	2.82E-08	NA	mr1191_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
vg1125216297	4.59E-09	1.15E-16	mr1191_2	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
vg1125216297	NA	1.11E-07	mr1498_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
vg1125216297	2.59E-06	NA	mr1662_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
vg1125216297	NA	5.28E-07	mr1925_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