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Detailed information for vg0824471012:

Variant ID: vg0824471012 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 24471012
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

AAGATATTCCCTGCACTGACGAGAGGGAGAGAGAGATAAAAATTGGGAGAGGATTCTAATAATTCGAGTGGACGTCCACCCGTTTATTGCATGTCAATTG[G/A]
ATGGTTACGAAAAATTTTCAAAAAAATTGACAAGATAGATCAATATGTAATATATCACTCCACAAACATGCAAGTTCAAATTCAACTTCTACAGATTGTA

Reverse complement sequence

TACAATCTGTAGAAGTTGAATTTGAACTTGCATGTTTGTGGAGTGATATATTACATATTGATCTATCTTGTCAATTTTTTTGAAAATTTTTCGTAACCAT[C/T]
CAATTGACATGCAATAAACGGGTGGACGTCCACTCGAATTATTAGAATCCTCTCCCAATTTTTATCTCTCTCTCCCTCTCGTCAGTGCAGGGAATATCTT

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	97.40%	1.80%	0.85%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	91.90%	5.60%	2.58%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.00%	0.13%	0.00%	NA
Temperate Japonica	767	85.40%	10.00%	4.56%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	96.30%	2.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0824471012	G -> A	LOC_Os08g38710.1	upstream_gene_variant ; 4134.0bp to feature; MODIFIER	silent_mutation	Average:45.275; most accessible tissue: Callus, score: 73.883	N	N	N	N
vg0824471012	G -> A	LOC_Os08g38700.1	downstream_gene_variant ; 3041.0bp to feature; MODIFIER	silent_mutation	Average:45.275; most accessible tissue: Callus, score: 73.883	N	N	N	N
vg0824471012	G -> A	LOC_Os08g38700-LOC_Os08g38710	intergenic_region ; MODIFIER	silent_mutation	Average:45.275; most accessible tissue: Callus, score: 73.883	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0824471012	3.28E-06	NA	mr1829_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