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Detailed information for vg1127692555:

Variant ID: vg1127692555 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27692555
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: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTGGAGAACCATTCAGAATCATTACTAGGGAAATGTGATGGTCTTCCTCTTGCTCTGGTCAGTGTCTCTGATTATCTGAAGAGCTCAACTGAGGCAAC[G/A]
GGAGAGTTGTGTGCAAAGCTATGCCGTGATCTGGGTTCTCATCTGACAGGAAACCATGGCCATGACAACTTTTCAGAACTCAGGAAGGTGCTTCTTGGCA

Reverse complement sequence

TGCCAAGAAGCACCTTCCTGAGTTCTGAAAAGTTGTCATGGCCATGGTTTCCTGTCAGATGAGAACCCAGATCACGGCATAGCTTTGCACACAACTCTCC[C/T]
GTTGCCTCAGTTGAGCTCTTCAGATAATCAGAGACACTGACCAGAGCAAGAGGAAGACCATCACATTTCCCTAGTAATGATTCTGAATGGTTCTCCAACT

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	71.30%	17.80%	0.72%	10.26%	NA
All Indica	2759	67.50%	22.90%	0.69%	8.92%	NA
All Japonica	1512	88.80%	3.00%	0.73%	7.47%	NA
Aus	269	35.70%	23.80%	0.37%	40.15%	NA
Indica I	595	72.30%	20.00%	0.34%	7.39%	NA
Indica II	465	52.90%	36.80%	0.43%	9.89%	NA
Indica III	913	75.50%	17.10%	0.55%	6.90%	NA
Indica Intermediate	786	63.10%	23.80%	1.27%	11.83%	NA
Temperate Japonica	767	94.40%	3.70%	0.39%	1.56%	NA
Tropical Japonica	504	80.00%	1.60%	1.19%	17.26%	NA
Japonica Intermediate	241	89.20%	4.10%	0.83%	5.81%	NA
VI/Aromatic	96	7.30%	79.20%	1.04%	12.50%	NA
Intermediate	90	68.90%	22.20%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127692555	G -> A	LOC_Os11g45770.1	upstream_gene_variant ; 2326.0bp to feature; MODIFIER	silent_mutation	Average:63.065; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N
vg1127692555	G -> A	LOC_Os11g45750.2	upstream_gene_variant ; 2267.0bp to feature; MODIFIER	silent_mutation	Average:63.065; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N
vg1127692555	G -> A	LOC_Os11g45750.1	intron_variant ; MODIFIER	silent_mutation	Average:63.065; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N
vg1127692555	G -> DEL	N	N	silent_mutation	Average:63.065; most accessible tissue: Zhenshan97 young leaf, score: 84.814	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127692555	1.31E-06	9.46E-10	mr1662_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
vg1127692555	7.59E-06	NA	mr1662_2	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
vg1127692555	6.33E-06	NA	mr1841_2	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
vg1127692555	7.70E-06	1.23E-06	mr1875_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
vg1127692555	2.69E-06	1.14E-06	mr1908_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