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Detailed information for vg0903244257:

Variant ID: vg0903244257 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3244257
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, T: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ACTACTGATAAGCGCACTGAATATTATTTTCCATTATATATGTGTTTCTAAAATAGAAGATAATGCATTACAATTATTTAAAGTACAAAGATTATTGACA[A/T]
TTACTTCGAAAAATTATTGTTGTCTGTAATAAATTAAGTGGATAAAATATAATAAGCAAATATATGATTTAAAATTAATTAATATTCTAATAATCATATA

Reverse complement sequence

TATATGATTATTAGAATATTAATTAATTTTAAATCATATATTTGCTTATTATATTTTATCCACTTAATTTATTACAGACAACAATAATTTTTCGAAGTAA[T/A]
TGTCAATAATCTTTGTACTTTAAATAATTGTAATGCATTATCTTCTATTTTAGAAACACATATATAATGGAAAATAATATTCAGTGCGCTTATCAGTAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.30%	25.90%	17.73%	14.09%	NA
All Indica	2759	14.20%	40.70%	23.02%	22.15%	NA
All Japonica	1512	96.20%	0.70%	0.99%	2.12%	NA
Aus	269	1.90%	26.00%	66.54%	5.58%	NA
Indica I	595	10.80%	32.90%	19.16%	37.14%	NA
Indica II	465	21.30%	24.70%	22.37%	31.61%	NA
Indica III	913	12.30%	60.20%	22.34%	5.15%	NA
Indica Intermediate	786	14.80%	33.20%	27.10%	24.94%	NA
Temperate Japonica	767	93.90%	0.40%	1.96%	3.78%	NA
Tropical Japonica	504	98.80%	1.00%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	1.20%	0.00%	0.83%	NA
VI/Aromatic	96	94.80%	2.10%	3.12%	0.00%	NA
Intermediate	90	63.30%	21.10%	6.67%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0903244257	A -> DEL	N	N	silent_mutation	Average:26.981; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0903244257	A -> T	LOC_Os09g06780.1	upstream_gene_variant ; 1652.0bp to feature; MODIFIER	silent_mutation	Average:26.981; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0903244257	A -> T	LOC_Os09g06790.1	downstream_gene_variant ; 655.0bp to feature; MODIFIER	silent_mutation	Average:26.981; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0903244257	A -> T	LOC_Os09g06780-LOC_Os09g06790	intergenic_region ; MODIFIER	silent_mutation	Average:26.981; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903244257	1.54E-06	NA	mr1279	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