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Detailed information for vg0824864741:

Variant ID: vg0824864741 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 24864741
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACTAAATGAGCAGAGGAATGGAAGCATGTACTACTATATAAGTAAAGGCCAAAAGACAAGCGGGAAATTAAAGAACAATAGTACTTTATAAACAAACAA[G/A]
CACCTCTCTATCCCAAGACTTGACACCATTTACCAATAAAAATTATCATGACAATCTAAGTTGGGGTTATCAAATTCTTCGTTATACATTTAACAAGCGC

Reverse complement sequence

GCGCTTGTTAAATGTATAACGAAGAATTTGATAACCCCAACTTAGATTGTCATGATAATTTTTATTGGTAAATGGTGTCAAGTCTTGGGATAGAGAGGTG[C/T]
TTGTTTGTTTATAAAGTACTATTGTTCTTTAATTTCCCGCTTGTCTTTTGGCCTTTACTTATATAGTAGTACATGCTTCCATTCCTCTGCTCATTTAGTA

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	92.70%	7.30%	0.04%	0.00%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.00%	NA
All Japonica	1512	79.20%	20.70%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.50%	2.50%	0.00%	0.00%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	66.50%	33.30%	0.20%	0.00%	NA
Japonica Intermediate	241	51.00%	49.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0824864741	G -> A	LOC_Os08g39350.1	upstream_gene_variant ; 1198.0bp to feature; MODIFIER	silent_mutation	Average:63.738; most accessible tissue: Callus, score: 83.271	N	N	N	N
vg0824864741	G -> A	LOC_Os08g39340.1	downstream_gene_variant ; 425.0bp to feature; MODIFIER	silent_mutation	Average:63.738; most accessible tissue: Callus, score: 83.271	N	N	N	N
vg0824864741	G -> A	LOC_Os08g39340-LOC_Os08g39350	intergenic_region ; MODIFIER	silent_mutation	Average:63.738; most accessible tissue: Callus, score: 83.271	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0824864741	NA	1.94E-06	mr1761	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
vg0824864741	2.74E-06	2.74E-06	mr1579_2	Jap_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