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Detailed information for vg1017706073:

Variant ID: vg1017706073 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 17706073
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCACCAAAACCCTGGTATATCAAACAGGCACAACCTTGAGAACATTTCTTATGAGCCTTGAAATTTGGTGGGGATTGTTAGAATAATTGGGCAAGGCC[C/T]
AAGATTATCCTATTAAATCTCAAAGGCCCATAATAAGTGTTAAGGATAATAATACCACCTCAGGATTTAAGCGAGGAATATCTCAACCTAAATAGGGAGT

Reverse complement sequence

ACTCCCTATTTAGGTTGAGATATTCCTCGCTTAAATCCTGAGGTGGTATTATTATCCTTAACACTTATTATGGGCCTTTGAGATTTAATAGGATAATCTT[G/A]
GGCCTTGCCCAATTATTCTAACAATCCCCACCAAATTTCAAGGCTCATAAGAAATGTTCTCAAGGTTGTGCCTGTTTGATATACCAGGGTTTTGGTGGAG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	5.70%	1.71%	0.00%	NA
All Indica	2759	88.00%	9.30%	2.68%	0.00%	NA
All Japonica	1512	99.50%	0.30%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.50%	0.70%	1.85%	0.00%	NA
Indica II	465	60.20%	31.00%	8.82%	0.00%	NA
Indica III	913	97.80%	1.60%	0.55%	0.00%	NA
Indica Intermediate	786	86.00%	11.80%	2.16%	0.00%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.80%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg1017706073	C -> T	LOC_Os10g33570.1	downstream_gene_variant ; 650.0bp to feature; MODIFIER	silent_mutation	Average:57.313; most accessible tissue: Zhenshan97 flower, score: 78.317	N	N	N	N
vg1017706073	C -> T	LOC_Os10g33570-LOC_Os10g33600	intergenic_region ; MODIFIER	silent_mutation	Average:57.313; most accessible tissue: Zhenshan97 flower, score: 78.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1017706073	1.84E-06	NA	mr1526	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
vg1017706073	NA	3.19E-06	mr1526	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