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Detailed information for vg1117147909:

Variant ID: vg1117147909 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17147909
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, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGGAAAACAATTTTCCTAGTAGTGAATCCAATGCAATGCGTTCTGATATGTTTGGCGACATTCTCATCTCTTTTTTTCCCTTCACCTCCACTAAATCT[G/A]
GCTAAACGACCATTTTTTTTTCATTTCGATAAGTATTCGATGGTAATCATAACCACCTCTGATATCTATTACTCATGCATGATGCATGACGATGCGAACA

Reverse complement sequence

TGTTCGCATCGTCATGCATCATGCATGAGTAATAGATATCAGAGGTGGTTATGATTACCATCGAATACTTATCGAAATGAAAAAAAAATGGTCGTTTAGC[C/T]
AGATTTAGTGGAGGTGAAGGGAAAAAAAGAGATGAGAATGTCGCCAAACATATCAGAACGCATTGCATTGGATTCACTACTAGGAAAATTGTTTTCCTAG

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	86.00%	10.50%	0.44%	3.07%	NA
All Indica	2759	82.10%	12.10%	0.65%	5.07%	NA
All Japonica	1512	99.50%	0.20%	0.07%	0.20%	NA
Aus	269	43.90%	55.80%	0.37%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	87.10%	10.80%	0.43%	1.72%	NA
Indica III	913	68.20%	19.50%	1.42%	10.84%	NA
Indica Intermediate	786	82.40%	13.00%	0.38%	4.20%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	5.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117147909	G -> A	LOC_Os11g29540.1	upstream_gene_variant ; 3694.0bp to feature; MODIFIER	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N
vg1117147909	G -> A	LOC_Os11g29560.1	upstream_gene_variant ; 1710.0bp to feature; MODIFIER	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N
vg1117147909	G -> A	LOC_Os11g29550.1	downstream_gene_variant ; 986.0bp to feature; MODIFIER	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N
vg1117147909	G -> A	LOC_Os11g29570.1	downstream_gene_variant ; 4967.0bp to feature; MODIFIER	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N
vg1117147909	G -> A	LOC_Os11g29550-LOC_Os11g29560	intergenic_region ; MODIFIER	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N
vg1117147909	G -> DEL	N	N	silent_mutation	Average:47.776; most accessible tissue: Zhenshan97 flag leaf, score: 71.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117147909	2.34E-06	1.85E-07	mr1271	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