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Detailed information for vg0208190322:

Variant ID: vg0208190322 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8190322
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

GAATCCTATAAAATTCCTACATAAATACTTTGATTCATAGGGGGCCTCAAAGGATTTCTTCCATGAGGTTCTAACTCTTGTTAAAATTCCTCCAAAACTT[G/A]
TATGAGAAGAGGCATTCCATAGGAATTTTATAGGATTCCATAGGGTTCATTCCTTTGATTCAAAGGGCTTTGTAGGAAAAAATCCTATAGGAATAAAATC

Reverse complement sequence

GATTTTATTCCTATAGGATTTTTTCCTACAAAGCCCTTTGAATCAAAGGAATGAACCCTATGGAATCCTATAAAATTCCTATGGAATGCCTCTTCTCATA[C/T]
AAGTTTTGGAGGAATTTTAACAAGAGTTAGAACCTCATGGAAGAAATCCTTTGAGGCCCCCTATGAATCAAAGTATTTATGTAGGAATTTTATAGGATTC

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	56.10%	17.90%	1.27%	24.74%	NA
All Indica	2759	43.60%	30.10%	1.59%	24.68%	NA
All Japonica	1512	70.20%	0.10%	0.79%	28.90%	NA
Aus	269	98.90%	0.00%	0.37%	0.74%	NA
Indica I	595	38.70%	30.40%	1.85%	29.08%	NA
Indica II	465	62.60%	24.70%	1.94%	10.75%	NA
Indica III	913	34.50%	34.00%	0.55%	31.00%	NA
Indica Intermediate	786	46.80%	28.50%	2.42%	22.26%	NA
Temperate Japonica	767	96.10%	0.00%	0.26%	3.65%	NA
Tropical Japonica	504	29.80%	0.20%	1.98%	68.06%	NA
Japonica Intermediate	241	72.60%	0.00%	0.00%	27.39%	NA
VI/Aromatic	96	62.50%	0.00%	0.00%	37.50%	NA
Intermediate	90	67.80%	14.40%	3.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208190322	G -> A	LOC_Os02g14770-LOC_Os02g14780	intergenic_region ; MODIFIER	silent_mutation	Average:57.604; most accessible tissue: Zhenshan97 root, score: 80.68	N	N	N	N
vg0208190322	G -> DEL	N	N	silent_mutation	Average:57.604; most accessible tissue: Zhenshan97 root, score: 80.68	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208190322	3.25E-06	3.51E-06	mr1171	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
vg0208190322	4.89E-06	1.21E-06	mr1171	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
vg0208190322	NA	3.21E-06	mr1780	Ind_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