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Detailed information for vg0908639557:

Variant ID: vg0908639557 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8639557
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, G: 0.20, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTGTTTTGGTTCATAACCACACTTGTGACGAGATTCCTTATCCATCATGTAGACCTCACATGTCATTGAGATAAAAGAGTGTGACAAGAGTGTCTCAT[T/G]
CTAGCTAAAGTGTGGCTCCAATTTTGTTAGCCACACATTAGGCAAGTTGGTCAAAACATTGTGTCAACCTTGCATAAATAGAAATACTCAACCAAACAGT

Reverse complement sequence

ACTGTTTGGTTGAGTATTTCTATTTATGCAAGGTTGACACAATGTTTTGACCAACTTGCCTAATGTGTGGCTAACAAAATTGGAGCCACACTTTAGCTAG[A/C]
ATGAGACACTCTTGTCACACTCTTTTATCTCAATGACATGTGAGGTCTACATGATGGATAAGGAATCTCGTCACAAGTGTGGTTATGAACCAAAACAAGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.20%	5.40%	17.03%	40.35%	NA
All Indica	2759	29.60%	6.60%	21.42%	42.37%	NA
All Japonica	1512	49.40%	2.60%	2.84%	45.17%	NA
Aus	269	16.00%	12.60%	57.62%	13.75%	NA
Indica I	595	15.80%	1.50%	16.30%	66.39%	NA
Indica II	465	61.90%	10.10%	10.97%	16.99%	NA
Indica III	913	19.30%	6.20%	32.75%	41.73%	NA
Indica Intermediate	786	32.80%	8.90%	18.32%	39.95%	NA
Temperate Japonica	767	84.90%	4.30%	0.13%	10.69%	NA
Tropical Japonica	504	4.00%	0.00%	7.34%	88.69%	NA
Japonica Intermediate	241	31.50%	2.50%	2.07%	63.90%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	65.60%	0.00%	14.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0908639557	T -> G	LOC_Os09g14600.1	upstream_gene_variant ; 4580.0bp to feature; MODIFIER	silent_mutation	Average:26.685; most accessible tissue: Minghui63 flower, score: 52.213	N	N	N	N
vg0908639557	T -> G	LOC_Os09g14590.1	intron_variant ; MODIFIER	silent_mutation	Average:26.685; most accessible tissue: Minghui63 flower, score: 52.213	N	N	N	N
vg0908639557	T -> DEL	N	N	silent_mutation	Average:26.685; most accessible tissue: Minghui63 flower, score: 52.213	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908639557	NA	3.11E-07	mr1040	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
vg0908639557	9.00E-06	9.00E-06	mr1230	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
vg0908639557	NA	3.85E-07	mr1785	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
vg0908639557	4.31E-06	5.99E-10	mr1836	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