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Detailed information for vg1125819702:

Variant ID: vg1125819702 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25819702
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTCCACTGATGTTTAGTAAAATTTGAATCACGCCACTATGTACACCTGGGACATGCTTGGAAAAGTTTTTTTTTAGCGCTTATCTTCTTCTTCCCCA[G/A]
CCTATCTTCTTCCTCTAGCGAAGAGGACACATGGATCGGGGGCTTGGAAATGGGGCTGGATGGTTTAATTTCCCCCTCTCTCTTGACGCCGATGGACCCC

Reverse complement sequence

GGGGTCCATCGGCGTCAAGAGAGAGGGGGAAATTAAACCATCCAGCCCCATTTCCAAGCCCCCGATCCATGTGTCCTCTTCGCTAGAGGAAGAAGATAGG[C/T]
TGGGGAAGAAGAAGATAAGCGCTAAAAAAAAACTTTTCCAAGCATGTCCCAGGTGTACATAGTGGCGTGATTCAAATTTTACTAAACATCAGTGGAACTA

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	68.90%	30.70%	0.36%	0.00%	NA
All Indica	2759	54.10%	45.50%	0.40%	0.00%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	54.60%	45.40%	0.00%	0.00%	NA
Indica I	595	58.50%	40.80%	0.67%	0.00%	NA
Indica II	465	25.60%	74.00%	0.43%	0.00%	NA
Indica III	913	68.10%	31.50%	0.33%	0.00%	NA
Indica Intermediate	786	51.30%	48.50%	0.25%	0.00%	NA
Temperate Japonica	767	96.10%	3.90%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	13.50%	5.21%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg1125819702	G -> A	LOC_Os11g42860.1	upstream_gene_variant ; 1684.0bp to feature; MODIFIER	silent_mutation	Average:41.7; most accessible tissue: Callus, score: 66.661	N	N	N	N
vg1125819702	G -> A	LOC_Os11g42870.1	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:41.7; most accessible tissue: Callus, score: 66.661	N	N	N	N
vg1125819702	G -> A	LOC_Os11g42860-LOC_Os11g42870	intergenic_region ; MODIFIER	silent_mutation	Average:41.7; most accessible tissue: Callus, score: 66.661	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125819702	NA	7.05E-10	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
vg1125819702	4.69E-07	8.83E-07	mr1662	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
vg1125819702	8.51E-09	2.09E-15	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
vg1125819702	1.23E-07	NA	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
vg1125819702	NA	3.25E-06	mr1471_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
vg1125819702	5.65E-06	7.32E-08	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