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Detailed information for vg1119967965:

Variant ID: vg1119967965 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19967965
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAATCATATTTTATCATCTAACAACAATGAAAATACAAATTATAAAAAAATTTCATATAAGACGGACAGTTAAAGTTGGACATGAAAACCTATAGTTT[G/A]
TCTTTTTTTGGATGGAGGGAGTAATCCTCTATTAGTTTCTCATCAATACTAGTAGTACGTACTACCGCTAGTCCGCTACTAGCTAACCGTGCCTCTGGCC

Reverse complement sequence

GGCCAGAGGCACGGTTAGCTAGTAGCGGACTAGCGGTAGTACGTACTACTAGTATTGATGAGAAACTAATAGAGGATTACTCCCTCCATCCAAAAAAAGA[C/T]
AAACTATAGGTTTTCATGTCCAACTTTAACTGTCCGTCTTATATGAAATTTTTTTATAATTTGTATTTTCATTGTTGTTAGATGATAAAATATGATTAAT

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	52.30%	47.10%	0.55%	0.00%	NA
All Indica	2759	43.50%	56.10%	0.40%	0.00%	NA
All Japonica	1512	62.90%	36.90%	0.20%	0.00%	NA
Aus	269	63.20%	33.80%	2.97%	0.00%	NA
Indica I	595	35.80%	64.20%	0.00%	0.00%	NA
Indica II	465	44.50%	55.10%	0.43%	0.00%	NA
Indica III	913	43.50%	56.20%	0.33%	0.00%	NA
Indica Intermediate	786	48.90%	50.40%	0.76%	0.00%	NA
Temperate Japonica	767	81.00%	18.90%	0.13%	0.00%	NA
Tropical Japonica	504	48.60%	51.20%	0.20%	0.00%	NA
Japonica Intermediate	241	35.30%	64.30%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	64.40%	34.40%	1.11%	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
vg1119967965	G -> A	LOC_Os11g34110.1	upstream_gene_variant ; 4666.0bp to feature; MODIFIER	silent_mutation	Average:45.135; most accessible tissue: Callus, score: 84.404	N	N	N	N
vg1119967965	G -> A	LOC_Os11g34120.1	downstream_gene_variant ; 3815.0bp to feature; MODIFIER	silent_mutation	Average:45.135; most accessible tissue: Callus, score: 84.404	N	N	N	N
vg1119967965	G -> A	LOC_Os11g34110-LOC_Os11g34120	intergenic_region ; MODIFIER	silent_mutation	Average:45.135; most accessible tissue: Callus, score: 84.404	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119967965	3.24E-06	NA	mr1632_2	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
vg1119967965	NA	9.42E-06	mr1693_2	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
vg1119967965	NA	6.50E-06	mr1788_2	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