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Detailed information for vg0502245051:

Variant ID: vg0502245051 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2245051
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TGAACTACTCCCTCAAAGATAATATATATACATAATTAAATAGAGTAAATAGGAGATGGTGATCGTGATTGTTTATTAAGGAGTAATGAGTAAAGAAGTT[G/A]
CTATATTATAGGATAATTCTTTTAGAGTTTATCGAATAAATCTTTAAATGCTAAAATTGTTATATTTTAAAACGAAAGGAGTAGCATACCGTGTATATAT

Reverse complement sequence

ATATATACACGGTATGCTACTCCTTTCGTTTTAAAATATAACAATTTTAGCATTTAAAGATTTATTCGATAAACTCTAAAAGAATTATCCTATAATATAG[C/T]
AACTTCTTTACTCATTACTCCTTAATAAACAATCACGATCACCATCTCCTATTTACTCTATTTAATTATGTATATATATTATCTTTGAGGGAGTAGTTCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.40%	49.40%	0.21%	0.00%	NA
All Indica	2759	25.60%	74.20%	0.22%	0.00%	NA
All Japonica	1512	94.40%	5.40%	0.13%	0.00%	NA
Aus	269	40.50%	59.50%	0.00%	0.00%	NA
Indica I	595	0.30%	99.70%	0.00%	0.00%	NA
Indica II	465	12.90%	87.10%	0.00%	0.00%	NA
Indica III	913	49.70%	49.70%	0.55%	0.00%	NA
Indica Intermediate	786	24.30%	75.60%	0.13%	0.00%	NA
Temperate Japonica	767	95.30%	4.60%	0.13%	0.00%	NA
Tropical Japonica	504	96.40%	3.60%	0.00%	0.00%	NA
Japonica Intermediate	241	87.60%	12.00%	0.41%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	62.20%	35.60%	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
vg0502245051	G -> A	LOC_Os05g04740.2	upstream_gene_variant ; 1784.0bp to feature; MODIFIER	silent_mutation	Average:66.92; most accessible tissue: Callus, score: 89.265	N	N	N	N
vg0502245051	G -> A	LOC_Os05g04740.1	upstream_gene_variant ; 1784.0bp to feature; MODIFIER	silent_mutation	Average:66.92; most accessible tissue: Callus, score: 89.265	N	N	N	N
vg0502245051	G -> A	LOC_Os05g04730-LOC_Os05g04740	intergenic_region ; MODIFIER	silent_mutation	Average:66.92; most accessible tissue: Callus, score: 89.265	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502245051	NA	6.53E-06	mr1109_2	Jap_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
vg0502245051	NA	1.76E-06	mr1754_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
vg0502245051	NA	5.70E-07	mr1819_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
vg0502245051	3.45E-06	1.96E-06	mr1865_2	Jap_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