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Detailed information for vg0203137179:

Variant ID: vg0203137179 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3137179
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.78, T: 0.24, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAACTTCCATTTTGAGCAGTTTTGAAAGCCAACGAGGTATTTTTTCCAGACAACGAGCAAGAAGGTACCGAAAGAACCTGAAGACTCTGAAAACCATC[A/T]
ACTATTGGTATGCCATCTGGCATGGCCTTGCCCTTGAAGTTGATTCCCATAATCAAAGTGTTGACTTTTTGCAGTTCTTGAGTGCATGAATTGCATTTGA

Reverse complement sequence

TCAAATGCAATTCATGCACTCAAGAACTGCAAAAAGTCAACACTTTGATTATGGGAATCAACTTCAAGGGCAAGGCCATGCCAGATGGCATACCAATAGT[T/A]
GATGGTTTTCAGAGTCTTCAGGTTCTTTCGGTACCTTCTTGCTCGTTGTCTGGAAAAAATACCTCGTTGGCTTTCAAAACTGCTCAAAATGGAAGTTTTG

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	55.10%	42.60%	0.00%	2.33%	NA
All Indica	2759	38.40%	59.00%	0.00%	2.54%	NA
All Japonica	1512	90.70%	9.10%	0.00%	0.20%	NA
Aus	269	17.10%	82.50%	0.00%	0.37%	NA
Indica I	595	53.40%	46.60%	0.00%	0.00%	NA
Indica II	465	53.50%	46.20%	0.00%	0.22%	NA
Indica III	913	17.90%	77.90%	0.00%	4.27%	NA
Indica Intermediate	786	42.00%	54.20%	0.00%	3.82%	NA
Temperate Japonica	767	84.50%	15.50%	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	70.00%	23.30%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0203137179	A -> T	LOC_Os02g06270.1	upstream_gene_variant ; 2194.0bp to feature; MODIFIER	silent_mutation	Average:47.338; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137179	A -> T	LOC_Os02g06290.1	upstream_gene_variant ; 4813.0bp to feature; MODIFIER	silent_mutation	Average:47.338; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137179	A -> T	LOC_Os02g06280.1	intron_variant ; MODIFIER	silent_mutation	Average:47.338; most accessible tissue: Callus, score: 84.278	N	N	N	N
vg0203137179	A -> DEL	N	N	silent_mutation	Average:47.338; most accessible tissue: Callus, score: 84.278	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203137179	NA	1.85E-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
vg0203137179	NA	5.52E-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
vg0203137179	NA	1.53E-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