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Detailed information for vg0208293749:

Variant ID: vg0208293749 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8293749
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

AACCTTAAATTTGGAGCTGATTTTAAGGTTTTTTTCATCGAAATTTATTTTTCAGCATTTGCTTTTATATCGCTAAGAACATGTATATAAAAGTTTTATT[C/T]
ACAAATTATTCTTTGTTTGCAAATATGCTGTTTCACTTATAATTCCGATGGCTCCGATAATGTCGATGGTAAAATTTAGAATTTCTCTTTTTCCTTCTAT

Reverse complement sequence

ATAGAAGGAAAAAGAGAAATTCTAAATTTTACCATCGACATTATCGGAGCCATCGGAATTATAAGTGAAACAGCATATTTGCAAACAAAGAATAATTTGT[G/A]
AATAAAACTTTTATATACATGTTCTTAGCGATATAAAAGCAAATGCTGAAAAATAAATTTCGATGAAAAAAACCTTAAAATCAGCTCCAAATTTAAGGTT

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	76.00%	23.90%	0.13%	0.00%	NA
All Indica	2759	60.50%	39.40%	0.14%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	64.50%	35.10%	0.34%	0.00%	NA
Indica II	465	43.70%	55.90%	0.43%	0.00%	NA
Indica III	913	65.90%	34.10%	0.00%	0.00%	NA
Indica Intermediate	786	60.90%	39.10%	0.00%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	21.10%	2.22%	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
vg0208293749	C -> T	LOC_Os02g14880.1	upstream_gene_variant ; 4061.0bp to feature; MODIFIER	silent_mutation	Average:64.691; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0208293749	C -> T	LOC_Os02g14890.1	downstream_gene_variant ; 486.0bp to feature; MODIFIER	silent_mutation	Average:64.691; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N
vg0208293749	C -> T	LOC_Os02g14890-LOC_Os02g14900	intergenic_region ; MODIFIER	silent_mutation	Average:64.691; most accessible tissue: Zhenshan97 panicle, score: 76.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208293749	NA	5.32E-06	mr1293	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
vg0208293749	6.86E-06	6.86E-06	mr1294	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
vg0208293749	NA	1.13E-06	mr1392	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
vg0208293749	NA	2.61E-06	mr1418	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
vg0208293749	4.53E-06	4.53E-06	mr1420	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