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Detailed information for vg0920652722:

Variant ID: vg0920652722 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20652722
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: 300. )

Flanking Sequence (100 bp) in Reference Genome:

TGGACGCTGTCAAAATGAAAAAAAAAAAAACTTTACATAGCTCCTCATTCGAAACAAAATCTGGATGACAGATCGGCTGCAAATCCGTCAATGTCTATCA[G/A]
TTTTGCTATAGAAACCTTTAAACGGCACAACACCTTTTCAAGGATTACACTTTCGTACATCAAATCTGAGAGAAGATCTTTCAACAGCCGAGACACAATA

Reverse complement sequence

TATTGTGTCTCGGCTGTTGAAAGATCTTCTCTCAGATTTGATGTACGAAAGTGTAATCCTTGAAAAGGTGTTGTGCCGTTTAAAGGTTTCTATAGCAAAA[C/T]
TGATAGACATTGACGGATTTGCAGCCGATCTGTCATCCAGATTTTGTTTCGAATGAGGAGCTATGTAAAGTTTTTTTTTTTTTCATTTTGACAGCGTCCA

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	97.50%	2.00%	0.55%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	92.30%	6.10%	1.65%	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	90.10%	6.90%	3.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	84.20%	14.90%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0920652722	G -> A	LOC_Os09g35880.1	upstream_gene_variant ; 2729.0bp to feature; MODIFIER	silent_mutation	Average:65.278; most accessible tissue: Callus, score: 87.013	N	N	N	N
vg0920652722	G -> A	LOC_Os09g35890.1	upstream_gene_variant ; 1985.0bp to feature; MODIFIER	silent_mutation	Average:65.278; most accessible tissue: Callus, score: 87.013	N	N	N	N
vg0920652722	G -> A	LOC_Os09g35890.2	upstream_gene_variant ; 1985.0bp to feature; MODIFIER	silent_mutation	Average:65.278; most accessible tissue: Callus, score: 87.013	N	N	N	N
vg0920652722	G -> A	LOC_Os09g35880-LOC_Os09g35890	intergenic_region ; MODIFIER	silent_mutation	Average:65.278; most accessible tissue: Callus, score: 87.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920652722	4.04E-06	4.03E-06	mr1833	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