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Detailed information for vg0804722355:

Variant ID: vg0804722355 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4722355
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TGACAATGTAAATACCAAAATTACATATGTAAGTCCTAAAATTACATATGTAAATCCCAAAATTACATCCTAATACATATGTAAGTGGGGTGTAACTACT[G/A]
TGTAAATTTGTAAATATATAAATAACTACCCCAGCAGTCACATACATGTAAGTGTGAACGCAGCAAAACAGCGGGCAGCGATGGTATGAGCACAATGGAT

Reverse complement sequence

ATCCATTGTGCTCATACCATCGCTGCCCGCTGTTTTGCTGCGTTCACACTTACATGTATGTGACTGCTGGGGTAGTTATTTATATATTTACAAATTTACA[C/T]
AGTAGTTACACCCCACTTACATATGTATTAGGATGTAATTTTGGGATTTACATATGTAATTTTAGGACTTACATATGTAATTTTGGTATTTACATTGTCA

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	78.50%	20.30%	0.40%	0.74%	NA
All Indica	2759	80.40%	17.80%	0.54%	1.27%	NA
All Japonica	1512	88.00%	11.70%	0.26%	0.00%	NA
Aus	269	32.30%	67.70%	0.00%	0.00%	NA
Indica I	595	93.30%	6.70%	0.00%	0.00%	NA
Indica II	465	59.80%	39.80%	0.22%	0.22%	NA
Indica III	913	87.30%	8.00%	1.42%	3.29%	NA
Indica Intermediate	786	74.70%	24.70%	0.13%	0.51%	NA
Temperate Japonica	767	90.70%	8.90%	0.39%	0.00%	NA
Tropical Japonica	504	86.30%	13.70%	0.00%	0.00%	NA
Japonica Intermediate	241	83.00%	16.60%	0.41%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	0.00%	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
vg0804722355	G -> A	LOC_Os08g08240.1	downstream_gene_variant ; 4474.0bp to feature; MODIFIER	silent_mutation	Average:67.645; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N
vg0804722355	G -> A	LOC_Os08g08250.1	downstream_gene_variant ; 3224.0bp to feature; MODIFIER	silent_mutation	Average:67.645; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N
vg0804722355	G -> A	LOC_Os08g08250-LOC_Os08g08260	intergenic_region ; MODIFIER	silent_mutation	Average:67.645; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N
vg0804722355	G -> DEL	N	N	silent_mutation	Average:67.645; most accessible tissue: Minghui63 panicle, score: 87.951	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804722355	2.82E-06	5.51E-08	mr1697	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
vg0804722355	NA	1.37E-06	mr1851	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
vg0804722355	NA	3.21E-06	mr1788_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