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Detailed information for vg0811281856:

Variant ID: vg0811281856 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11281856
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTGGAGATGATGCCAATGGGATGTACATTCTCCTTGTCCAATCTTAGGGCTTGTTCAGTTTGTAGGATTATCAAAATGTAGAAAAAGAGAAAAGATAG[G/A]
AATAATATAGGAATGCATGTGCAAACCTAAGGATTGGAAAACATATGAAATTTTCCAATGGTTATGTAGCAAACAATCCAAAGGATTGAAAACATTGGGT

Reverse complement sequence

ACCCAATGTTTTCAATCCTTTGGATTGTTTGCTACATAACCATTGGAAAATTTCATATGTTTTCCAATCCTTAGGTTTGCACATGCATTCCTATATTATT[C/T]
CTATCTTTTCTCTTTTTCTACATTTTGATAATCCTACAAACTGAACAAGCCCTAAGATTGGACAAGGAGAATGTACATCCCATTGGCATCATCTCCAAAT

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	56.00%	43.70%	0.28%	0.08%	NA
All Indica	2759	85.50%	14.00%	0.33%	0.14%	NA
All Japonica	1512	6.70%	93.30%	0.00%	0.00%	NA
Aus	269	52.80%	46.80%	0.37%	0.00%	NA
Indica I	595	97.60%	2.40%	0.00%	0.00%	NA
Indica II	465	91.20%	8.80%	0.00%	0.00%	NA
Indica III	913	72.50%	26.60%	0.55%	0.33%	NA
Indica Intermediate	786	88.20%	11.20%	0.51%	0.13%	NA
Temperate Japonica	767	5.10%	94.90%	0.00%	0.00%	NA
Tropical Japonica	504	6.30%	93.70%	0.00%	0.00%	NA
Japonica Intermediate	241	12.90%	87.10%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	41.10%	55.60%	3.33%	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
vg0811281856	G -> A	LOC_Os08g18920.1	upstream_gene_variant ; 2647.0bp to feature; MODIFIER	silent_mutation	Average:69.23; most accessible tissue: Zhenshan97 panicle, score: 90.268	N	N	N	N
vg0811281856	G -> A	LOC_Os08g18930.1	upstream_gene_variant ; 714.0bp to feature; MODIFIER	silent_mutation	Average:69.23; most accessible tissue: Zhenshan97 panicle, score: 90.268	N	N	N	N
vg0811281856	G -> A	LOC_Os08g18920-LOC_Os08g18930	intergenic_region ; MODIFIER	silent_mutation	Average:69.23; most accessible tissue: Zhenshan97 panicle, score: 90.268	N	N	N	N
vg0811281856	G -> DEL	N	N	silent_mutation	Average:69.23; most accessible tissue: Zhenshan97 panicle, score: 90.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811281856	NA	1.09E-07	mr1238	Ind_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
vg0811281856	NA	1.55E-06	mr1309	Ind_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
vg0811281856	NA	2.35E-09	mr1379	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
vg0811281856	3.63E-06	2.12E-06	mr1401	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
vg0811281856	NA	1.97E-08	mr1841	Ind_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
vg0811281856	5.63E-07	5.63E-07	mr1900	Ind_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