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Detailed information for vg0818648206:

Variant ID: vg0818648206 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18648206
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, G: 0.15, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

ACACGCCACTTACACATGTAATTACTATATAATTTTGAGACTTACATATGTATTTTTGAAACTTACATTATAAATACACTAAATTTACATATGTAATTTA[T/G]
GGACTTACAATGTAAATAAATGCTGACTATTTTTTAATAAAAAATATGGTGCTATAAATATAGCTATTCCCTTTATTATATATGTAAGTTACTTTTATCA

Reverse complement sequence

TGATAAAAGTAACTTACATATATAATAAAGGGAATAGCTATATTTATAGCACCATATTTTTTATTAAAAAATAGTCAGCATTTATTTACATTGTAAGTCC[A/C]
TAAATTACATATGTAAATTTAGTGTATTTATAATGTAAGTTTCAAAAATACATATGTAAGTCTCAAAATTATATAGTAATTACATGTGTAAGTGGCGTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.00%	37.70%	0.59%	1.78%	NA
All Indica	2759	87.40%	8.60%	1.01%	2.97%	NA
All Japonica	1512	15.70%	84.30%	0.00%	0.00%	NA
Aus	269	50.90%	49.10%	0.00%	0.00%	NA
Indica I	595	82.70%	16.60%	0.34%	0.34%	NA
Indica II	465	84.70%	4.70%	3.66%	6.88%	NA
Indica III	913	94.70%	2.40%	0.00%	2.85%	NA
Indica Intermediate	786	84.00%	12.10%	1.15%	2.80%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	40.30%	59.70%	0.00%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	89.60%	0.00%	0.00%	NA
Intermediate	90	42.20%	55.60%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818648206	T -> G	LOC_Os08g30300-LOC_Os08g30310	intergenic_region ; MODIFIER	silent_mutation	Average:21.842; most accessible tissue: Callus, score: 40.138	N	N	N	N
vg0818648206	T -> DEL	N	N	silent_mutation	Average:21.842; most accessible tissue: Callus, score: 40.138	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818648206	NA	4.72E-07	mr1320	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
vg0818648206	NA	9.99E-06	mr1351	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
vg0818648206	NA	2.32E-08	mr1438	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
vg0818648206	NA	3.23E-09	mr1836	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