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Detailed information for vg0808527211:

Variant ID: vg0808527211 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8527211
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.07, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AATACTCCACTTTCATATTATCTAATTTTATTGGATGCATACATTACATTTACTAGGACGATCCAAACTACAAGATGATAATAATTTTTTCTTAGTCTTT[A/G]
GATTAATAGTAGTTGTGCTTTATATTTTGGAATGGAGGAAGTAATAATATTAGGATATGTCATATCTTATAATACCTTCGTCCCAAAATATAATAATTTT

Reverse complement sequence

AAAATTATTATATTTTGGGACGAAGGTATTATAAGATATGACATATCCTAATATTATTACTTCCTCCATTCCAAAATATAAAGCACAACTACTATTAATC[T/C]
AAAGACTAAGAAAAAATTATTATCATCTTGTAGTTTGGATCGTCCTAGTAAATGTAATGTATGCATCCAATAAAATTAGATAATATGAAAGTGGAGTATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	35.40%	0.23%	1.61%	NA
All Indica	2759	55.70%	43.80%	0.33%	0.14%	NA
All Japonica	1512	71.40%	28.20%	0.07%	0.40%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	52.60%	46.90%	0.50%	0.00%	NA
Indica II	465	49.90%	49.90%	0.00%	0.22%	NA
Indica III	913	54.80%	44.70%	0.22%	0.33%	NA
Indica Intermediate	786	62.60%	36.90%	0.51%	0.00%	NA
Temperate Japonica	767	82.10%	17.70%	0.13%	0.00%	NA
Tropical Japonica	504	72.20%	27.20%	0.00%	0.60%	NA
Japonica Intermediate	241	35.30%	63.50%	0.00%	1.24%	NA
VI/Aromatic	96	29.20%	5.20%	0.00%	65.62%	NA
Intermediate	90	68.90%	26.70%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808527211	A -> G	LOC_Os08g14230-LOC_Os08g14250	intergenic_region ; MODIFIER	silent_mutation	Average:73.128; most accessible tissue: Callus, score: 89.988	N	N	N	N
vg0808527211	A -> DEL	N	N	silent_mutation	Average:73.128; most accessible tissue: Callus, score: 89.988	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808527211	9.19E-06	NA	mr1097_2	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