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Detailed information for vg1108064089:

Variant ID: vg1108064089 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8064089
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CCACACCATTGCATCTCCCGAGTAAGCTAGCTAGACAATTATATCTTGAATACTATATTGAAAAGCTGGTACTCAAATGATCAAAGTGAAGTAAAGTACC[G/A]
TAAATATATTGAGAAGAATATTCTATAAATAGTACATGTCTTACAAAAGAAGGAAAAACTAGTAGAGCCATACCCGAACTCTTCCGAAGACTCTATTCTA

Reverse complement sequence

TAGAATAGAGTCTTCGGAAGAGTTCGGGTATGGCTCTACTAGTTTTTCCTTCTTTTGTAAGACATGTACTATTTATAGAATATTCTTCTCAATATATTTA[C/T]
GGTACTTTACTTCACTTTGATCATTTGAGTACCAGCTTTTCAATATAGTATTCAAGATATAATTGTCTAGCTAGCTTACTCGGGAGATGCAATGGTGTGG

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	57.70%	42.20%	0.04%	0.00%	NA
All Indica	2759	30.70%	69.30%	0.07%	0.00%	NA
All Japonica	1512	97.20%	2.80%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	13.30%	86.70%	0.00%	0.00%	NA
Indica II	465	7.50%	92.50%	0.00%	0.00%	NA
Indica III	913	51.30%	48.60%	0.11%	0.00%	NA
Indica Intermediate	786	33.60%	66.30%	0.13%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg1108064089	G -> A	LOC_Os11g14370.1	upstream_gene_variant ; 4798.0bp to feature; MODIFIER	silent_mutation	Average:42.166; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg1108064089	G -> A	LOC_Os11g14350.1	downstream_gene_variant ; 3637.0bp to feature; MODIFIER	silent_mutation	Average:42.166; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N
vg1108064089	G -> A	LOC_Os11g14360.1	intron_variant ; MODIFIER	silent_mutation	Average:42.166; most accessible tissue: Zhenshan97 flag leaf, score: 58.104	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108064089	NA	2.28E-07	mr1136	Jap_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
vg1108064089	NA	2.94E-20	mr1422	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
vg1108064089	NA	4.82E-08	mr1929	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
vg1108064089	4.62E-06	6.29E-09	mr1136_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
vg1108064089	NA	1.16E-15	mr1720_2	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