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Detailed information for vg1110727944:

Variant ID: vg1110727944 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10727944
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GCAAGTTACTTAACTTACGCCCAAAGTTTTACACAAAGGTAGATTGCATCTCTATATGTTAGGAATAGTGGGAAAGCACATAAAACATTGCAAACTTCGA[G/A]
TTCATATTATGGACCTTACATAGGAATTATTGTAAACGTATTTGATTCCACATGGATGAAATTATGGCGAGTGCACTACGAGACTTTGAACCTATATATC

Reverse complement sequence

GATATATAGGTTCAAAGTCTCGTAGTGCACTCGCCATAATTTCATCCATGTGGAATCAAATACGTTTACAATAATTCCTATGTAAGGTCCATAATATGAA[C/T]
TCGAAGTTTGCAATGTTTTATGTGCTTTCCCACTATTCCTAACATATAGAGATGCAATCTACCTTTGTGTAAAACTTTGGGCGTAAGTTAAGTAACTTGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.50%	36.40%	0.19%	0.00%	NA
All Indica	2759	94.10%	5.60%	0.25%	0.00%	NA
All Japonica	1512	4.20%	95.70%	0.07%	0.00%	NA
Aus	269	93.70%	5.90%	0.37%	0.00%	NA
Indica I	595	95.50%	4.40%	0.17%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	98.10%	1.90%	0.00%	0.00%	NA
Indica Intermediate	786	85.80%	13.70%	0.51%	0.00%	NA
Temperate Japonica	767	3.50%	96.50%	0.00%	0.00%	NA
Tropical Japonica	504	5.80%	94.20%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.30%	0.41%	0.00%	NA
VI/Aromatic	96	29.20%	70.80%	0.00%	0.00%	NA
Intermediate	90	64.40%	35.60%	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
vg1110727944	G -> A	LOC_Os11g18870.1	upstream_gene_variant ; 4978.0bp to feature; MODIFIER	silent_mutation	Average:40.837; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N
vg1110727944	G -> A	LOC_Os11g18860-LOC_Os11g18870	intergenic_region ; MODIFIER	silent_mutation	Average:40.837; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110727944	NA	4.22E-11	mr1595	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
vg1110727944	NA	8.50E-28	mr1723	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
vg1110727944	NA	2.28E-11	mr1595_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
vg1110727944	NA	2.01E-08	mr1600_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
vg1110727944	2.48E-06	NA	mr1758_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
vg1110727944	3.04E-06	NA	mr1758_2	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