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Detailed information for vg0915181272:

Variant ID: vg0915181272 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 15181272
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCTTTTTTCTCTTCAAATAAAATTTTCTCTCAAATTACTTATCCGATCTATAATCCAATTACACCATTGTGTTCGTTACAATTAAATCTTCACAACAA[A/G]
ATCTTACATGATTATATTACGATGAAAAAATATTTATATTTGTAAATTATTTTTATTATATACGTAAGTTACTTTTATCATATATATATATATATATATA

Reverse complement sequence

TATATATATATATATATATATGATAAAAGTAACTTACGTATATAATAAAAATAATTTACAAATATAAATATTTTTTCATCGTAATATAATCATGTAAGAT[T/C]
TTGTTGTGAAGATTTAATTGTAACGAACACAATGGTGTAATTGGATTATAGATCGGATAAGTAATTTGAGAGAAAATTTTATTTGAAGAGAAAAAAGGCA

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	35.80%	0.50%	4.30%	59.37%	NA
All Indica	2759	1.40%	0.70%	6.52%	91.30%	NA
All Japonica	1512	99.00%	0.10%	0.40%	0.53%	NA
Aus	269	2.20%	0.40%	3.72%	93.68%	NA
Indica I	595	1.20%	0.20%	5.55%	93.11%	NA
Indica II	465	2.40%	0.00%	4.09%	93.55%	NA
Indica III	913	0.70%	1.30%	9.20%	88.83%	NA
Indica Intermediate	786	2.00%	0.90%	5.60%	91.48%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.20%	0.00%	0.40%	0.40%	NA
Japonica Intermediate	241	97.10%	0.40%	1.66%	0.83%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	64.40%	1.10%	6.67%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0915181272	A -> G	LOC_Os09g25340.1	upstream_gene_variant ; 4867.0bp to feature; MODIFIER	silent_mutation	Average:30.637; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0915181272	A -> G	LOC_Os09g25330-LOC_Os09g25340	intergenic_region ; MODIFIER	silent_mutation	Average:30.637; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg0915181272	A -> DEL	N	N	silent_mutation	Average:30.637; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0915181272	1.49E-08	NA	mr1155	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
vg0915181272	NA	1.07E-86	mr1504	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
vg0915181272	NA	4.68E-85	mr1672	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