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Detailed information for vg0320596106:

Variant ID: vg0320596106 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20596106
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTACTTAACTCCAGTGCAGGTCCAAACTCGCCTTTGGGTATGTTAGCGTGCCAATTGATTTGATTCTACAATCAACAAGAAATAAAGACAAAGAAACC[G/A]
CGATTAAACCTATAAACGATAGCCGATCGGCTAAGTGCCGATGGCATATCATTTATCTTTGAGCCGATGTCATATATGTATCGATCGGCAGTCATGAATA

Reverse complement sequence

TATTCATGACTGCCGATCGATACATATATGACATCGGCTCAAAGATAAATGATATGCCATCGGCACTTAGCCGATCGGCTATCGTTTATAGGTTTAATCG[C/T]
GGTTTCTTTGTCTTTATTTCTTGTTGATTGTAGAATCAAATCAATTGGCACGCTAACATACCCAAAGGCGAGTTTGGACCTGCACTGGAGTTAAGTAGAT

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	92.90%	7.00%	0.11%	0.00%	NA
All Indica	2759	88.50%	11.40%	0.14%	0.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	60.80%	38.50%	0.67%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.50%	8.50%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	2.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0320596106	G -> A	LOC_Os03g37140.1	upstream_gene_variant ; 2683.0bp to feature; MODIFIER	silent_mutation	Average:29.112; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N
vg0320596106	G -> A	LOC_Os03g37170.1	upstream_gene_variant ; 932.0bp to feature; MODIFIER	silent_mutation	Average:29.112; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N
vg0320596106	G -> A	LOC_Os03g37180.1	upstream_gene_variant ; 2052.0bp to feature; MODIFIER	silent_mutation	Average:29.112; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N
vg0320596106	G -> A	LOC_Os03g37170-LOC_Os03g37180	intergenic_region ; MODIFIER	silent_mutation	Average:29.112; most accessible tissue: Zhenshan97 flower, score: 44.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320596106	1.38E-07	9.57E-08	mr1172_2	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