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Detailed information for vg0203137069:

Variant ID: vg0203137069 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3137069
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, T: 0.36, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

ACTGGGAGATCCCTTCTAAGATTGTTGTTTGATATATCTATGAAGTAGAGGAAGTTCAGGCCATGGATCCAGTCTGATATTGGTCCAGTGAGTTAATTGT[A/T]
GGATAGATCCAAAACTTCCATTTTGAGCAGTTTTGAAAGCCAACGAGGTATTTTTTCCAGACAACGAGCAAGAAGGTACCGAAAGAACCTGAAGACTCTG

Reverse complement sequence

CAGAGTCTTCAGGTTCTTTCGGTACCTTCTTGCTCGTTGTCTGGAAAAAATACCTCGTTGGCTTTCAAAACTGCTCAAAATGGAAGTTTTGGATCTATCC[T/A]
ACAATTAACTCACTGGACCAATATCAGACTGGATCCATGGCCTGAACTTCCTCTACTTCATAGATATATCAAACAACAATCTTAGAAGGGATCTCCCAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.90%	42.80%	0.04%	2.26%	NA
All Indica	2759	38.30%	59.20%	0.04%	2.46%	NA
All Japonica	1512	90.60%	9.20%	0.00%	0.20%	NA
Aus	269	17.10%	82.50%	0.00%	0.37%	NA
Indica I	595	53.10%	46.90%	0.00%	0.00%	NA
Indica II	465	53.50%	46.20%	0.00%	0.22%	NA
Indica III	913	17.90%	77.90%	0.11%	4.16%	NA
Indica Intermediate	786	42.00%	54.30%	0.00%	3.69%	NA
Temperate Japonica	767	84.40%	15.60%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	5.00%	0.00%	1.24%	NA
VI/Aromatic	96	64.60%	4.20%	0.00%	31.25%	NA
Intermediate	90	66.70%	26.70%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203137069	A -> T	LOC_Os02g06270.1	upstream_gene_variant ; 2084.0bp to feature; MODIFIER	silent_mutation	Average:52.96; most accessible tissue: Callus, score: 82.405	N	N	N	N
vg0203137069	A -> T	LOC_Os02g06290.1	upstream_gene_variant ; 4923.0bp to feature; MODIFIER	silent_mutation	Average:52.96; most accessible tissue: Callus, score: 82.405	N	N	N	N
vg0203137069	A -> T	LOC_Os02g06280.1	intron_variant ; MODIFIER	silent_mutation	Average:52.96; most accessible tissue: Callus, score: 82.405	N	N	N	N
vg0203137069	A -> DEL	N	N	silent_mutation	Average:52.96; most accessible tissue: Callus, score: 82.405	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203137069	NA	1.09E-06	mr1517_2	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
vg0203137069	NA	5.89E-09	mr1582_2	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
vg0203137069	NA	1.19E-06	mr1582_2	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