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Detailed information for vg0812018672:

Variant ID: vg0812018672 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12018672
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.07, C: 0.03, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

AATAAAACGCCTAAAGAAATTGTTCAATTTAACCTTGAGCTGAACCCTAATTAATGAATGCATTTGATATTTGGAAATGGCATGGTGGAATTTTTCTTGA[G/A]
TTCCCGATGTTTAATGCATTAACAAGATTTTTAATGGAATTTTCATAGCCTTGAAAATAATTTTATCCAATTAAAATCAATTATCTTCAATAAATAAATC

Reverse complement sequence

GATTTATTTATTGAAGATAATTGATTTTAATTGGATAAAATTATTTTCAAGGCTATGAAAATTCCATTAAAAATCTTGTTAATGCATTAAACATCGGGAA[C/T]
TCAAGAAAAATTCCACCATGCCATTTCCAAATATCAAATGCATTCATTAATTAGGGTTCAGCTCAAGGTTAAATTGAACAATTTCTTTAGGCGTTTTATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.40%	7.50%	0.76%	52.26%	NA
All Indica	2759	15.80%	9.60%	1.16%	73.43%	NA
All Japonica	1512	84.70%	5.00%	0.13%	10.19%	NA
Aus	269	4.10%	1.10%	0.37%	94.42%	NA
Indica I	595	33.90%	2.50%	1.51%	62.02%	NA
Indica II	465	16.60%	4.90%	1.51%	76.99%	NA
Indica III	913	2.00%	17.30%	0.55%	80.18%	NA
Indica Intermediate	786	17.60%	8.90%	1.40%	72.14%	NA
Temperate Japonica	767	95.80%	0.30%	0.13%	3.78%	NA
Tropical Japonica	504	68.50%	12.90%	0.00%	18.65%	NA
Japonica Intermediate	241	83.00%	3.70%	0.41%	12.86%	NA
VI/Aromatic	96	88.50%	5.20%	0.00%	6.25%	NA
Intermediate	90	58.90%	6.70%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812018672	G -> A	LOC_Os08g20050.1	downstream_gene_variant ; 3590.0bp to feature; MODIFIER	silent_mutation	Average:10.183; most accessible tissue: Callus, score: 51.397	N	N	N	N
vg0812018672	G -> A	LOC_Os08g20050-LOC_Os08g20060	intergenic_region ; MODIFIER	silent_mutation	Average:10.183; most accessible tissue: Callus, score: 51.397	N	N	N	N
vg0812018672	G -> DEL	N	N	silent_mutation	Average:10.183; most accessible tissue: Callus, score: 51.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812018672	4.83E-06	4.83E-06	mr1345	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
vg0812018672	NA	4.13E-07	mr1886	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