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Detailed information for vg1114037213:

Variant ID: vg1114037213 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14037213
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGTAAATTTCTGGGTTTGGTTATCACATCAGATTTATAAACATACATTTAAAATATTAAACGTACTCTAATAACAAAATAAATTACAGATTCTGCTAG[G/T]
AAACCGTGAGATGAATTTATTAAGCCTAATTAATCCGTCATTAGCAAATATTTACTATAGCACCACATTATCAAATCATGACGCAATTAGGCTTAAAAGA

Reverse complement sequence

TCTTTTAAGCCTAATTGCGTCATGATTTGATAATGTGGTGCTATAGTAAATATTTGCTAATGACGGATTAATTAGGCTTAATAAATTCATCTCACGGTTT[C/A]
CTAGCAGAATCTGTAATTTATTTTGTTATTAGAGTACGTTTAATATTTTAAATGTATGTTTATAAATCTGATGTGATAACCAAACCCAGAAATTTACCCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.40%	35.10%	0.40%	19.09%	NA
All Indica	2759	19.60%	51.90%	0.51%	28.05%	NA
All Japonica	1512	97.40%	0.60%	0.13%	1.85%	NA
Aus	269	0.00%	72.90%	0.37%	26.77%	NA
Indica I	595	29.70%	64.50%	0.34%	5.38%	NA
Indica II	465	2.40%	40.40%	0.43%	56.77%	NA
Indica III	913	26.50%	50.20%	0.11%	23.22%	NA
Indica Intermediate	786	14.00%	51.00%	1.15%	33.84%	NA
Temperate Japonica	767	96.90%	0.40%	0.00%	2.74%	NA
Tropical Japonica	504	97.40%	1.00%	0.40%	1.19%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	90.60%	6.20%	0.00%	3.12%	NA
Intermediate	90	52.20%	17.80%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1114037213	G -> T	LOC_Os11g24590.1	upstream_gene_variant ; 1689.0bp to feature; MODIFIER	silent_mutation	Average:23.349; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1114037213	G -> T	LOC_Os11g24600.1	downstream_gene_variant ; 1136.0bp to feature; MODIFIER	silent_mutation	Average:23.349; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1114037213	G -> T	LOC_Os11g24580-LOC_Os11g24600	intergenic_region ; MODIFIER	silent_mutation	Average:23.349; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg1114037213	G -> DEL	N	N	silent_mutation	Average:23.349; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114037213	NA	2.39E-09	mr1097	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
vg1114037213	2.82E-06	NA	mr1350_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