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Detailed information for vg0812330953:

Variant ID: vg0812330953 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12330953
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.81, G: 0.18, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCATGCTGAATAAGCCTTACTATATTTGCTCTTAAAAGATAGAAAGATAGGATAACATCACGAACTGAATTGCAGCGGTCTAGGCTACTCACACCGGC[T/G]
CATTGCCAAATCAAAATGGGGCTATTCAGACTAAAATCAAAATGGATGAATGATCCATTATAAAACAACGAAGAAACGAGTAAAACAATAGGACAGATTT

Reverse complement sequence

AAATCTGTCCTATTGTTTTACTCGTTTCTTCGTTGTTTTATAATGGATCATTCATCCATTTTGATTTTAGTCTGAATAGCCCCATTTTGATTTGGCAATG[A/C]
GCCGGTGTGAGTAGCCTAGACCGCTGCAATTCAGTTCGTGATGTTATCCTATCTTTCTATCTTTTAAGAGCAAATATAGTAAGGCTTATTCAGCATGCGA

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	89.10%	10.50%	0.02%	0.32%	NA
All Indica	2759	90.10%	9.40%	0.04%	0.47%	NA
All Japonica	1512	85.40%	14.60%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	97.80%	1.80%	0.00%	0.34%	NA
Indica II	465	92.30%	7.70%	0.00%	0.00%	NA
Indica III	913	83.40%	15.80%	0.11%	0.77%	NA
Indica Intermediate	786	90.80%	8.70%	0.00%	0.51%	NA
Temperate Japonica	767	91.70%	8.30%	0.00%	0.00%	NA
Tropical Japonica	504	73.00%	27.00%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812330953	T -> G	LOC_Os08g20544.1	downstream_gene_variant ; 573.0bp to feature; MODIFIER	silent_mutation	Average:75.245; most accessible tissue: Callus, score: 91.094	N	N	N	N
vg0812330953	T -> G	LOC_Os08g20500-LOC_Os08g20544	intergenic_region ; MODIFIER	silent_mutation	Average:75.245; most accessible tissue: Callus, score: 91.094	N	N	N	N
vg0812330953	T -> DEL	N	N	silent_mutation	Average:75.245; most accessible tissue: Callus, score: 91.094	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812330953	4.27E-07	1.07E-08	mr1915	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
vg0812330953	NA	6.14E-06	mr1200_2	Jap_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