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Detailed information for vg0729360051:

Variant ID: vg0729360051 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 29360051
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAGGACCTAAACGAGTGATAAGCAAGTTTAGCGACCGGGATGATACAGTCGAACAAGTATGAGGACCTGAACGGGTCGATTTGCGAGTTTAGGGACCG[G/A]
GATGACACAGCGGTACAAGTTTAGGGACCGATGATGGACTTTACTCATTAGGTAATTAAGGCTCTGTATGTATAAACATCGCCAATTAATTGGAACATTC

Reverse complement sequence

GAATGTTCCAATTAATTGGCGATGTTTATACATACAGAGCCTTAATTACCTAATGAGTAAAGTCCATCATCGGTCCCTAAACTTGTACCGCTGTGTCATC[C/T]
CGGTCCCTAAACTCGCAAATCGACCCGTTCAGGTCCTCATACTTGTTCGACTGTATCATCCCGGTCGCTAAACTTGCTTATCACTCGTTTAGGTCCTCCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.50%	41.50%	0.04%	0.00%	NA
All Indica	2759	89.90%	10.10%	0.04%	0.00%	NA
All Japonica	1512	6.70%	93.30%	0.00%	0.00%	NA
Aus	269	55.00%	45.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	92.70%	7.30%	0.00%	0.00%	NA
Indica III	913	84.20%	15.70%	0.11%	0.00%	NA
Indica Intermediate	786	88.20%	11.80%	0.00%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	28.20%	71.80%	0.00%	0.00%	NA
VI/Aromatic	96	3.10%	96.90%	0.00%	0.00%	NA
Intermediate	90	36.70%	62.20%	1.11%	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
vg0729360051	G -> A	LOC_Os07g49030.1	upstream_gene_variant ; 2736.0bp to feature; MODIFIER	silent_mutation	Average:69.655; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N
vg0729360051	G -> A	LOC_Os07g49040.1	upstream_gene_variant ; 3601.0bp to feature; MODIFIER	silent_mutation	Average:69.655; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N
vg0729360051	G -> A	LOC_Os07g49030.2	upstream_gene_variant ; 3134.0bp to feature; MODIFIER	silent_mutation	Average:69.655; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N
vg0729360051	G -> A	LOC_Os07g49030-LOC_Os07g49040	intergenic_region ; MODIFIER	silent_mutation	Average:69.655; most accessible tissue: Minghui63 panicle, score: 85.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729360051	2.53E-06	1.45E-07	mr1897	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
vg0729360051	NA	1.22E-12	mr1914	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
vg0729360051	NA	9.11E-07	mr1914	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