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Detailed information for vg0922634062:

Variant ID: vg0922634062 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22634062
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTTTGTCCATCGTCGTGTCGGTTTATTTCCCACACGACGCAGCCGCGCTCACTCAGCCAATCTACGCATTCGCTTACAGACATACGCATGCCCAGCT[G/A]
ACCATCTGCCCCTTACGGCTTGTTTGGCAACTTAAGGGAAGGGGATTGGGAGTTTACACGAGGGAATTGATGGTGAGATTAAGATGGGAATTTGATTTTT

Reverse complement sequence

AAAAATCAAATTCCCATCTTAATCTCACCATCAATTCCCTCGTGTAAACTCCCAATCCCCTTCCCTTAAGTTGCCAAACAAGCCGTAAGGGGCAGATGGT[C/T]
AGCTGGGCATGCGTATGTCTGTAAGCGAATGCGTAGATTGGCTGAGTGAGCGCGGCTGCGTCGTGTGGGAAATAAACCGACACGACGATGGACAAAAATA

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	53.50%	46.40%	0.08%	0.00%	NA
All Indica	2759	23.20%	76.70%	0.14%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	82.90%	17.10%	0.00%	0.00%	NA
Indica I	595	33.60%	66.20%	0.17%	0.00%	NA
Indica II	465	9.70%	90.30%	0.00%	0.00%	NA
Indica III	913	18.70%	81.30%	0.00%	0.00%	NA
Indica Intermediate	786	28.40%	71.20%	0.38%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0922634062	G -> A	LOC_Os09g39350.1	upstream_gene_variant ; 567.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922634062	G -> A	LOC_Os09g39360.1	upstream_gene_variant ; 1416.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922634062	G -> A	LOC_Os09g39350.2	upstream_gene_variant ; 567.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922634062	G -> A	LOC_Os09g39370.1	downstream_gene_variant ; 4550.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0922634062	G -> A	LOC_Os09g39350-LOC_Os09g39360	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922634062	3.15E-15	NA	mr1865	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
vg0922634062	8.18E-15	9.87E-18	mr1865	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
vg0922634062	1.64E-09	NA	mr1865_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
vg0922634062	5.15E-10	1.41E-12	mr1865_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