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Detailed information for vg0228079966:

Variant ID: vg0228079966 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28079966
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.07, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TGTACTGCTCAACATGTTTGGGCCATCATTGGGGAATCTAAATGACACGGCAGTATTTCTTGTTCTCTTACTACCAAAATAAATAACATGATCACCTTCA[T/C]
AATCTCTTGTAAACTACAAGAAACACAAAATCCTTCTAAAGCACAAACTTTAATTTCTATGATTTGTTGCCCTCTACCCCTTTACTTGGCTCCTCTAATG

Reverse complement sequence

CATTAGAGGAGCCAAGTAAAGGGGTAGAGGGCAACAAATCATAGAAATTAAAGTTTGTGCTTTAGAAGGATTTTGTGTTTCTTGTAGTTTACAAGAGATT[A/G]
TGAAGGTGATCATGTTATTTATTTTGGTAGTAAGAGAACAAGAAATACTGCCGTGTCATTTAGATTCCCCAATGATGGCCCAAACATGTTGAGCAGTACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.80%	41.10%	0.17%	0.00%	NA
All Indica	2759	93.60%	6.30%	0.14%	0.00%	NA
All Japonica	1512	0.70%	99.30%	0.00%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	97.50%	2.40%	0.17%	0.00%	NA
Indica II	465	97.40%	2.20%	0.43%	0.00%	NA
Indica III	913	88.70%	11.20%	0.11%	0.00%	NA
Indica Intermediate	786	94.00%	6.00%	0.00%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	35.60%	60.00%	4.44%	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
vg0228079966	T -> C	LOC_Os02g46070.1	downstream_gene_variant ; 4664.0bp to feature; MODIFIER	silent_mutation	Average:46.333; most accessible tissue: Callus, score: 81.178	N	N	N	N
vg0228079966	T -> C	LOC_Os02g46080.1	intron_variant ; MODIFIER	silent_mutation	Average:46.333; most accessible tissue: Callus, score: 81.178	N	N	N	N
vg0228079966	T -> C	LOC_Os02g46080.2	intron_variant ; MODIFIER	silent_mutation	Average:46.333; most accessible tissue: Callus, score: 81.178	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228079966	NA	1.55E-75	mr1629	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