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Detailed information for vg0827029665:

Variant ID: vg0827029665 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27029665
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GAGATGATATACTAAAGTAACAAAGATGCTGATTACTGAATTGCTTCCAATGTAAGTAAAAAGAGGGAGTGCTTTAACAGAAAATATCAAATTAAATAGA[T/A]
GGATTAAGTCCAAGGATACATTTGTATTCCACTGATAATAGCTCCAAAAAGTCCCAACATTGCCATCAACTCAATTCTGTTGCTTTTCTTGACCAGGTAC

Reverse complement sequence

GTACCTGGTCAAGAAAAGCAACAGAATTGAGTTGATGGCAATGTTGGGACTTTTTGGAGCTATTATCAGTGGAATACAAATGTATCCTTGGACTTAATCC[A/T]
TCTATTTAATTTGATATTTTCTGTTAAAGCACTCCCTCTTTTTACTTACATTGGAAGCAATTCAGTAATCAGCATCTTTGTTACTTTAGTATATCATCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	15.30%	0.02%	0.00%	NA
All Indica	2759	77.60%	22.40%	0.00%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	72.90%	26.80%	0.37%	0.00%	NA
Indica I	595	85.70%	14.30%	0.00%	0.00%	NA
Indica II	465	70.50%	29.50%	0.00%	0.00%	NA
Indica III	913	74.00%	26.00%	0.00%	0.00%	NA
Indica Intermediate	786	79.90%	20.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0827029665	T -> A	LOC_Os08g42710.1	downstream_gene_variant ; 2436.0bp to feature; MODIFIER	silent_mutation	Average:43.771; most accessible tissue: Callus, score: 60.543	N	N	N	N
vg0827029665	T -> A	LOC_Os08g42720.1	intron_variant ; MODIFIER	silent_mutation	Average:43.771; most accessible tissue: Callus, score: 60.543	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827029665	2.26E-06	NA	mr1955_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