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Detailed information for vg0403670833:

Variant ID: vg0403670833 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3670833
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: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GAACTTGCCCGTCAGCGGTCACTCCGCCGGCGGTCGACGGCTGGATGAATAATTCAGTTTTGAGTTTGTTATGCATGCACGAGAGATGTGGCGAGCTGCA[G/A]
GAGTAGACGACCGCGTCAGGCGTGCGTTGTGGGCGTGAGTTTTGCACGGCATTGGATCCAGGAGTTCCGGATCGTGGGATGGCGCGATTGTAGGCTTGGA

Reverse complement sequence

TCCAAGCCTACAATCGCGCCATCCCACGATCCGGAACTCCTGGATCCAATGCCGTGCAAAACTCACGCCCACAACGCACGCCTGACGCGGTCGTCTACTC[C/T]
TGCAGCTCGCCACATCTCTCGTGCATGCATAACAAACTCAAAACTGAATTATTCATCCAGCCGTCGACCGCCGGCGGAGTGACCGCTGACGGGCAAGTTC

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	50.40%	26.50%	0.47%	22.64%	NA
All Indica	2759	48.30%	44.10%	0.29%	7.29%	NA
All Japonica	1512	44.20%	0.60%	0.86%	54.30%	NA
Aus	269	92.60%	0.00%	0.00%	7.43%	NA
Indica I	595	7.70%	90.40%	0.00%	1.85%	NA
Indica II	465	41.70%	48.00%	0.43%	9.89%	NA
Indica III	913	74.90%	18.00%	0.11%	7.01%	NA
Indica Intermediate	786	52.00%	37.20%	0.64%	10.18%	NA
Temperate Japonica	767	45.00%	0.50%	1.30%	53.19%	NA
Tropical Japonica	504	34.70%	0.40%	0.40%	64.48%	NA
Japonica Intermediate	241	61.80%	1.20%	0.41%	36.51%	NA
VI/Aromatic	96	85.40%	2.10%	0.00%	12.50%	NA
Intermediate	90	54.40%	26.70%	1.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403670833	G -> DEL	N	N	silent_mutation	Average:24.916; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0403670833	G -> A	LOC_Os04g06960.1	upstream_gene_variant ; 25.0bp to feature; MODIFIER	silent_mutation	Average:24.916; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0403670833	G -> A	LOC_Os04g06970.1	upstream_gene_variant ; 809.0bp to feature; MODIFIER	silent_mutation	Average:24.916; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0403670833	G -> A	LOC_Os04g06950.1	downstream_gene_variant ; 3498.0bp to feature; MODIFIER	silent_mutation	Average:24.916; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N
vg0403670833	G -> A	LOC_Os04g06960-LOC_Os04g06970	intergenic_region ; MODIFIER	silent_mutation	Average:24.916; most accessible tissue: Zhenshan97 flag leaf, score: 66.327	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403670833	1.77E-06	NA	mr1907_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