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Detailed information for vg0232306661:

Variant ID: vg0232306661 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32306661
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTAGGAAAGTGTGTTTAGTGTCCGATAAGGACTTTATATTTTCCTTTTATCTTTAGGTTAGTTTCTTTCTTGTCTGACAAGGACTTGTATCAACCCAT[G/A]
GGTATAAATATGTACACCCGGGGTCTATGTAATATATCCTCACGATCAATACAATTCGGCGCATCGCCACCTTTTACCTTTTCTACTTTATTTTATCGTC

Reverse complement sequence

GACGATAAAATAAAGTAGAAAAGGTAAAAGGTGGCGATGCGCCGAATTGTATTGATCGTGAGGATATATTACATAGACCCCGGGTGTACATATTTATACC[C/T]
ATGGGTTGATACAAGTCCTTGTCAGACAAGAAAGAAACTAACCTAAAGATAAAAGGAAAATATAAAGTCCTTATCGGACACTAAACACACTTTCCTAAAG

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	93.30%	6.00%	0.70%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	80.40%	17.50%	2.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.60%	0.00%	0.00%	NA
Temperate Japonica	767	66.10%	30.00%	3.91%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	86.30%	13.30%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	15.60%	1.11%	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
vg0232306661	G -> A	LOC_Os02g52830.1	upstream_gene_variant ; 2679.0bp to feature; MODIFIER	silent_mutation	Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0232306661	G -> A	LOC_Os02g52840.1	downstream_gene_variant ; 4138.0bp to feature; MODIFIER	silent_mutation	Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0232306661	G -> A	LOC_Os02g52830-LOC_Os02g52840	intergenic_region ; MODIFIER	silent_mutation	Average:35.05; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232306661	5.97E-07	NA	mr1486	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
vg0232306661	6.51E-06	3.74E-11	mr1486	Jap_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