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Detailed information for vg0816206848:

Variant ID: vg0816206848 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16206848
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGAATTCTTGCAACTCTTTTTATGACTCTTGGGAATTTGTTTTCAAAAATAAAATTGTTTTAAAAGCTCAATCCTCCAATTGACTTTACCTTATACCT[A/G]
CCAAGGCCATATGCAAAGTATATTAATGATTAACCTTATCATGCATATGACTCCTTGACATTATATTGAGCTTGGTCAAATTTGTGTGACTTGTGTTAGA

Reverse complement sequence

TCTAACACAAGTCACACAAATTTGACCAAGCTCAATATAATGTCAAGGAGTCATATGCATGATAAGGTTAATCATTAATATACTTTGCATATGGCCTTGG[T/C]
AGGTATAAGGTAAAGTCAATTGGAGGATTGAGCTTTTAAAACAATTTTATTTTTGAAAACAAATTCCCAAGAGTCATAAAAAGAGTTGCAAGAATTCCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.80%	3.90%	12.23%	22.05%	NA
All Indica	2759	56.30%	6.10%	18.67%	18.92%	NA
All Japonica	1512	76.10%	0.10%	0.73%	23.02%	NA
Aus	269	20.10%	5.60%	16.36%	57.99%	NA
Indica I	595	66.60%	3.40%	9.75%	20.34%	NA
Indica II	465	56.30%	4.30%	16.56%	22.80%	NA
Indica III	913	45.50%	9.40%	28.15%	16.98%	NA
Indica Intermediate	786	61.10%	5.50%	15.65%	17.81%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	41.30%	0.20%	1.39%	57.14%	NA
Japonica Intermediate	241	77.60%	0.40%	1.66%	20.33%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	76.70%	0.00%	7.78%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816206848	A -> G	LOC_Os08g26670.1	upstream_gene_variant ; 3036.0bp to feature; MODIFIER	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 23.956	N	N	N	N
vg0816206848	A -> G	LOC_Os08g26650.1	downstream_gene_variant ; 3628.0bp to feature; MODIFIER	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 23.956	N	N	N	N
vg0816206848	A -> G	LOC_Os08g26660.1	downstream_gene_variant ; 731.0bp to feature; MODIFIER	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 23.956	N	N	N	N
vg0816206848	A -> G	LOC_Os08g26660-LOC_Os08g26670	intergenic_region ; MODIFIER	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 23.956	N	N	N	N
vg0816206848	A -> DEL	N	N	silent_mutation	Average:7.401; most accessible tissue: Callus, score: 23.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816206848	4.23E-06	1.30E-06	mr1152	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