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Detailed information for vg0608352271:

Variant ID: vg0608352271 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8352271
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, G: 0.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ACTACCAATGTTTTATCATGTAATAACAATAAAAATACTAATTATAAATTTTTTCCAAATAAGACGAACGGTCAAACGTTAGACATGAACAGTGCTAAAA[C/G]
TGTACTTATTTTAGGACGGAGGGAGTATTATGAAACAAACCATTTAGCAATTTAGGAAATGTGCTTACGAGACATAAGAAAATTTGCTTGGCCAAGTAGC

Reverse complement sequence

GCTACTTGGCCAAGCAAATTTTCTTATGTCTCGTAAGCACATTTCCTAAATTGCTAAATGGTTTGTTTCATAATACTCCCTCCGTCCTAAAATAAGTACA[G/C]
TTTTAGCACTGTTCATGTCTAACGTTTGACCGTTCGTCTTATTTGGAAAAAATTTATAATTAGTATTTTTATTGTTATTACATGATAAAACATTGGTAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	82.10%	17.90%	0.00%	0.00%	NA
All Indica	2759	69.60%	30.40%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	61.00%	39.00%	0.00%	0.00%	NA
Indica II	465	94.60%	5.40%	0.00%	0.00%	NA
Indica III	913	54.80%	45.20%	0.00%	0.00%	NA
Indica Intermediate	786	78.40%	21.60%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0608352271	C -> G	LOC_Os06g14750-LOC_Os06g14770	intergenic_region ; MODIFIER	silent_mutation	Average:48.84; most accessible tissue: Zhenshan97 flower, score: 70.434	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608352271	5.66E-08	6.60E-08	mr1719	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