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Detailed information for vg0806495774:

Variant ID: vg0806495774 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6495774
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: 105. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTATTAAATCAAGAATTTTTCTTGGGATCCCCCATTACATGGCCTTAAGGATCTATTTATAACCCTGTTATAGGTCCTCCTTTTAGGGCTTAGGTTTT[G/A]
CAGGGGAATTTACATGGTTGCCCTTATGAAAGGGACATTTACATGGGTACACAGTGTCATTTGCATACATGGGCCTCTAATGGGCCTGGTTGGCAAATGC

Reverse complement sequence

GCATTTGCCAACCAGGCCCATTAGAGGCCCATGTATGCAAATGACACTGTGTACCCATGTAAATGTCCCTTTCATAAGGGCAACCATGTAAATTCCCCTG[C/T]
AAAACCTAAGCCCTAAAAGGAGGACCTATAACAGGGTTATAAATAGATCCTTAAGGCCATGTAATGGGGGATCCCAAGAAAAATTCTTGATTTAATACAT

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	53.30%	3.30%	9.39%	34.00%	NA
All Indica	2759	29.80%	5.00%	12.18%	53.10%	NA
All Japonica	1512	97.80%	0.10%	0.20%	1.98%	NA
Aus	269	49.80%	4.10%	35.69%	10.41%	NA
Indica I	595	53.40%	1.20%	5.55%	39.83%	NA
Indica II	465	20.20%	16.60%	20.65%	42.58%	NA
Indica III	913	16.90%	2.80%	11.50%	68.78%	NA
Indica Intermediate	786	32.40%	3.40%	12.98%	51.15%	NA
Temperate Japonica	767	98.00%	0.10%	0.26%	1.56%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	97.10%	0.00%	0.41%	2.49%	NA
VI/Aromatic	96	33.30%	0.00%	6.25%	60.42%	NA
Intermediate	90	62.20%	5.60%	3.33%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806495774	G -> A	LOC_Os08g11040.1	upstream_gene_variant ; 872.0bp to feature; MODIFIER	silent_mutation	Average:15.567; most accessible tissue: Callus, score: 57.966	N	N	N	N
vg0806495774	G -> A	LOC_Os08g11020.1	downstream_gene_variant ; 2379.0bp to feature; MODIFIER	silent_mutation	Average:15.567; most accessible tissue: Callus, score: 57.966	N	N	N	N
vg0806495774	G -> A	LOC_Os08g11050.1	downstream_gene_variant ; 4942.0bp to feature; MODIFIER	silent_mutation	Average:15.567; most accessible tissue: Callus, score: 57.966	N	N	N	N
vg0806495774	G -> A	LOC_Os08g11030.1	intron_variant ; MODIFIER	silent_mutation	Average:15.567; most accessible tissue: Callus, score: 57.966	N	N	N	N
vg0806495774	G -> DEL	N	N	silent_mutation	Average:15.567; most accessible tissue: Callus, score: 57.966	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806495774	NA	1.82E-06	mr1904	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