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Detailed information for vg0811628032:

Variant ID: vg0811628032 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11628032
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.02, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGTCTTTGGAAGTGAAAGAGAGCACATGTAGTAAGTGGGAAGGGAGGAAAGAACTGCATTCACAATGGTCAATCTGTCCCCATAAGATAACAAAGCAG[T/C]
GGTTGATGAGAGTCTTCTCTCTACTCTATCAACTAGAGGAGCAAAATCTATAACTCTTGGTCTTGTGGTTCCAAGAGGAAGACACAGATAAGTAAAAGGT

Reverse complement sequence

ACCTTTTACTTATCTGTGTCTTCCTCTTGGAACCACAAGACCAAGAGTTATAGATTTTGCTCCTCTAGTTGATAGAGTAGAGAGAAGACTCTCATCAACC[A/G]
CTGCTTTGTTATCTTATGGGGACAGATTGACCATTGTGAATGCAGTTCTTTCCTCCCTTCCCACTTACTACATGTGCTCTCTTTCACTTCCAAAGACAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.70%	6.60%	34.49%	25.20%	NA
All Indica	2759	7.80%	8.30%	43.89%	39.98%	NA
All Japonica	1512	82.50%	0.30%	12.70%	4.43%	NA
Aus	269	1.50%	26.40%	71.00%	1.12%	NA
Indica I	595	2.20%	6.40%	37.48%	53.95%	NA
Indica II	465	7.50%	6.20%	53.55%	32.69%	NA
Indica III	913	12.70%	8.50%	41.73%	37.02%	NA
Indica Intermediate	786	6.50%	10.80%	45.55%	37.15%	NA
Temperate Japonica	767	88.50%	0.30%	10.95%	0.26%	NA
Tropical Japonica	504	79.40%	0.40%	13.29%	6.94%	NA
Japonica Intermediate	241	70.10%	0.40%	17.01%	12.45%	NA
VI/Aromatic	96	84.40%	2.10%	9.38%	4.17%	NA
Intermediate	90	48.90%	5.60%	30.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811628032	T -> C	LOC_Os08g19460.1	upstream_gene_variant ; 2681.0bp to feature; MODIFIER	silent_mutation	Average:26.762; most accessible tissue: Callus, score: 44.43	N	N	N	N
vg0811628032	T -> C	LOC_Os08g19470.1	upstream_gene_variant ; 2358.0bp to feature; MODIFIER	silent_mutation	Average:26.762; most accessible tissue: Callus, score: 44.43	N	N	N	N
vg0811628032	T -> C	LOC_Os08g19460-LOC_Os08g19470	intergenic_region ; MODIFIER	silent_mutation	Average:26.762; most accessible tissue: Callus, score: 44.43	N	N	N	N
vg0811628032	T -> DEL	N	N	silent_mutation	Average:26.762; most accessible tissue: Callus, score: 44.43	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811628032	1.10E-06	1.10E-06	mr1883	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