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Detailed information for vg0206177435:

Variant ID: vg0206177435 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6177435
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.50, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAGTTTCAAAAAGTCCTCGTCCGTTCAACAAAATGTCCGTGTCCGATTCCATACAAAATATGATCAATGAATTTAAAAAAACGGTTTAAACATGAAT[G/A]
ACGTATCAAAATTTTAGCAAAAACATCTTCAATTTTTATAATAGTAGAGATTAATATAATTTTTTAAAAAAATCTATGTTACACAATTAGGGTTAATATG

Reverse complement sequence

CATATTAACCCTAATTGTGTAACATAGATTTTTTTAAAAAATTATATTAATCTCTACTATTATAAAAATTGAAGATGTTTTTGCTAAAATTTTGATACGT[C/T]
ATTCATGTTTAAACCGTTTTTTTAAATTCATTGATCATATTTTGTATGGAATCGGACACGGACATTTTGTTGAACGGACGAGGACTTTTTGAAACTGTGA

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	67.10%	32.70%	0.13%	0.00%	NA
All Indica	2759	54.70%	45.20%	0.14%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	27.90%	71.40%	0.74%	0.00%	NA
Indica I	595	83.20%	16.60%	0.17%	0.00%	NA
Indica II	465	60.40%	39.40%	0.22%	0.00%	NA
Indica III	913	37.00%	62.90%	0.11%	0.00%	NA
Indica Intermediate	786	50.30%	49.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.80%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	39.60%	60.40%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg0206177435	G -> A	LOC_Os02g11920.1	upstream_gene_variant ; 3647.0bp to feature; MODIFIER	silent_mutation	Average:53.915; most accessible tissue: Callus, score: 80.871	N	N	N	N
vg0206177435	G -> A	LOC_Os02g11920-LOC_Os02g11930	intergenic_region ; MODIFIER	silent_mutation	Average:53.915; most accessible tissue: Callus, score: 80.871	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206177435	NA	1.71E-06	mr1004	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
vg0206177435	NA	4.54E-06	mr1006	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
vg0206177435	NA	3.32E-06	mr1007	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
vg0206177435	NA	4.51E-06	mr1052	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
vg0206177435	NA	4.71E-06	mr1097	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
vg0206177435	NA	9.56E-10	mr1004_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
vg0206177435	NA	2.69E-07	mr1006_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
vg0206177435	NA	3.89E-11	mr1065_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
vg0206177435	7.06E-06	NA	mr1091_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
vg0206177435	4.60E-06	1.33E-11	mr1091_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
vg0206177435	NA	8.01E-06	mr1092_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
vg0206177435	NA	2.81E-06	mr1097_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
vg0206177435	NA	2.59E-08	mr1112_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
vg0206177435	NA	4.61E-06	mr1154_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
vg0206177435	2.44E-06	NA	mr1877_2	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
vg0206177435	7.20E-06	3.40E-08	mr1877_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