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Detailed information for vg1017447725:

Variant ID: vg1017447725 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17447725
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTGACATATCACATATTGATCTATTCTACTATTTATTTTAAAATTTTTTTGATGACTTTTTAAGTGACATGAAAAATGAGGGGATATCCCCTTAAAG[G/T]
ATAATTTGAGTTTTCCCTTTTTCTTTGTTAATATAGGGTTTTCACAGTCTGTTACTCCTACTAGAGTATTAGCTACCTACTGCTTGACAGTTAAATGCCT

Reverse complement sequence

AGGCATTTAACTGTCAAGCAGTAGGTAGCTAATACTCTAGTAGGAGTAACAGACTGTGAAAACCCTATATTAACAAAGAAAAAGGGAAAACTCAAATTAT[C/A]
CTTTAAGGGGATATCCCCTCATTTTTCATGTCACTTAAAAAGTCATCAAAAAAATTTTAAAATAAATAGTAGAATAGATCAATATGTGATATGTCACTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.50%	10.20%	0.28%	0.00%	NA
All Indica	2759	93.80%	5.90%	0.33%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	11.20%	87.70%	1.12%	0.00%	NA
Indica I	595	97.10%	2.70%	0.17%	0.00%	NA
Indica II	465	96.10%	3.70%	0.22%	0.00%	NA
Indica III	913	91.60%	8.20%	0.22%	0.00%	NA
Indica Intermediate	786	92.40%	7.00%	0.64%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	38.50%	61.50%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	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
vg1017447725	G -> T	LOC_Os10g33250.1	downstream_gene_variant ; 1226.0bp to feature; MODIFIER	silent_mutation	Average:43.547; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg1017447725	G -> T	LOC_Os10g33250.2	downstream_gene_variant ; 1270.0bp to feature; MODIFIER	silent_mutation	Average:43.547; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N
vg1017447725	G -> T	LOC_Os10g33240-LOC_Os10g33250	intergenic_region ; MODIFIER	silent_mutation	Average:43.547; most accessible tissue: Zhenshan97 flower, score: 74.953	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017447725	NA	6.30E-06	mr1808	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
vg1017447725	NA	3.63E-06	mr1158_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
vg1017447725	4.20E-06	4.20E-06	mr1983_2	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