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Detailed information for vg0613699047:

Variant ID: vg0613699047 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13699047
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, T: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTTTAAAATTACATTTTGGGACAAAAAATGACTTAAAATAAAAAAAACTCAACTACAAAGTTGTAGATCGCGTCGAGGGCTACAAGTTTGATATAAA[G/T]
TTTGTCTTTATTAGAGTTCACATGAAAAATTTATGAATTATTTTTAAATATAAAGTCTCTAGACTGTCTTATTTGACCCAGATGATATTCAAATCTAAGT

Reverse complement sequence

ACTTAGATTTGAATATCATCTGGGTCAAATAAGACAGTCTAGAGACTTTATATTTAAAAATAATTCATAAATTTTTCATGTGAACTCTAATAAAGACAAA[C/A]
TTTATATCAAACTTGTAGCCCTCGACGCGATCTACAACTTTGTAGTTGAGTTTTTTTTATTTTAAGTCATTTTTTGTCCCAAAATGTAATTTTAAAATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	33.80%	0.53%	0.00%	NA
All Indica	2759	96.60%	2.70%	0.72%	0.00%	NA
All Japonica	1512	7.90%	92.00%	0.13%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	97.00%	2.40%	0.67%	0.00%	NA
Indica II	465	97.60%	1.30%	1.08%	0.00%	NA
Indica III	913	98.50%	1.00%	0.55%	0.00%	NA
Indica Intermediate	786	93.50%	5.70%	0.76%	0.00%	NA
Temperate Japonica	767	3.50%	96.20%	0.26%	0.00%	NA
Tropical Japonica	504	14.70%	85.30%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	47.80%	48.90%	3.33%	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
vg0613699047	G -> T	LOC_Os06g23460.1	upstream_gene_variant ; 1121.0bp to feature; MODIFIER	silent_mutation	Average:24.883; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0613699047	G -> T	LOC_Os06g23480.1	upstream_gene_variant ; 2025.0bp to feature; MODIFIER	silent_mutation	Average:24.883; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0613699047	G -> T	LOC_Os06g23470.1	downstream_gene_variant ; 665.0bp to feature; MODIFIER	silent_mutation	Average:24.883; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg0613699047	G -> T	LOC_Os06g23460-LOC_Os06g23470	intergenic_region ; MODIFIER	silent_mutation	Average:24.883; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613699047	1.12E-06	NA	mr1682	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
vg0613699047	4.13E-06	NA	mr1754	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