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Detailed information for vg0810149802:

Variant ID: vg0810149802 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 10149802
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ACGGATGGAGTGTTACCTTCCCATGATGTCATTACCTGCCTTGTCATTGTTGTAGCCGTACTGGTAAGTGGGCATTGCGCTTAGAAATTTCCATGGCTCC[G/A]
ATGCACACGGATCCCATTGGATGATTGCATGCTGCTTCTTGCCTGCAGGCAGGGGCGGATCCAAGGGGTAGGCTTCATCAGGCTCAAGTTTGCCTTCCGA

Reverse complement sequence

TCGGAAGGCAAACTTGAGCCTGATGAAGCCTACCCCTTGGATCCGCCCCTGCCTGCAGGCAAGAAGCAGCATGCAATCATCCAATGGGATCCGTGTGCAT[C/T]
GGAGCCATGGAAATTTCTAAGCGCAATGCCCACTTACCAGTACGGCTACAACAATGACAAGGCAGGTAATGACATCATGGGAAGGTAACACTCCATCCGT

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	93.70%	6.30%	0.02%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.00%	0.00%	NA
All Japonica	1512	87.30%	12.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	92.60%	7.40%	0.00%	0.00%	NA
Tropical Japonica	504	77.40%	22.60%	0.00%	0.00%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	1.04%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0810149802	G -> A	LOC_Os08g16590.1	upstream_gene_variant ; 26.0bp to feature; MODIFIER	silent_mutation	Average:49.029; most accessible tissue: Callus, score: 68.779	N	N	N	N
vg0810149802	G -> A	LOC_Os08g16600.1	upstream_gene_variant ; 2269.0bp to feature; MODIFIER	silent_mutation	Average:49.029; most accessible tissue: Callus, score: 68.779	N	N	N	N
vg0810149802	G -> A	LOC_Os08g16590-LOC_Os08g16600	intergenic_region ; MODIFIER	silent_mutation	Average:49.029; most accessible tissue: Callus, score: 68.779	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0810149802	NA	7.51E-11	mr1070	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
vg0810149802	NA	1.03E-06	mr1940	Jap_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
vg0810149802	NA	2.08E-06	mr1045_2	Jap_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
vg0810149802	2.40E-06	NA	mr1085_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
vg0810149802	4.69E-06	NA	mr1107_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
vg0810149802	NA	5.47E-06	mr1204_2	Jap_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
vg0810149802	NA	3.56E-06	mr1252_2	Jap_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
vg0810149802	NA	8.43E-06	mr1617_2	Jap_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
vg0810149802	4.63E-06	NA	mr1771_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
vg0810149802	NA	4.88E-06	mr1788_2	Jap_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