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Detailed information for vg1110586892:

Variant ID: vg1110586892 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10586892
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.55, A: 0.45, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCAACTATAGTTTTGAGCTGAGTTCAAACTTTTTAACAGTGTATTGCTCTTTTGGATTTCACAAAGAAAACAAAACGAAAGAGAGGAACGTGGGACCT[G/A]
CGTGGGTACATACTTATTTACACCTAGAAGTGGGGACTTTTAGAGATAAATTAAATTGGTAGTTTTTTAAGATAGATTCAATGCATGGATAAAACAATGG

Reverse complement sequence

CCATTGTTTTATCCATGCATTGAATCTATCTTAAAAAACTACCAATTTAATTTATCTCTAAAAGTCCCCACTTCTAGGTGTAAATAAGTATGTACCCACG[C/T]
AGGTCCCACGTTCCTCTCTTTCGTTTTGTTTTCTTTGTGAAATCCAAAAGAGCAATACACTGTTAAAAAGTTTGAACTCAGCTCAAAACTATAGTTGGGA

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	77.30%	20.20%	2.56%	0.00%	NA
All Indica	2759	67.70%	28.60%	3.66%	0.00%	NA
All Japonica	1512	97.00%	2.20%	0.79%	0.00%	NA
Aus	269	82.90%	15.20%	1.86%	0.00%	NA
Indica I	595	62.90%	28.40%	8.74%	0.00%	NA
Indica II	465	45.80%	51.00%	3.23%	0.00%	NA
Indica III	913	80.60%	18.40%	0.99%	0.00%	NA
Indica Intermediate	786	69.30%	27.50%	3.18%	0.00%	NA
Temperate Japonica	767	97.50%	1.30%	1.17%	0.00%	NA
Tropical Japonica	504	96.80%	3.00%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.83%	0.00%	NA
VI/Aromatic	96	33.30%	66.70%	0.00%	0.00%	NA
Intermediate	90	68.90%	27.80%	3.33%	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
vg1110586892	G -> A	LOC_Os11g18690.1	upstream_gene_variant ; 3906.0bp to feature; MODIFIER	silent_mutation	Average:12.309; most accessible tissue: Zhenshan97 flag leaf, score: 18.943	N	N	N	N
vg1110586892	G -> A	LOC_Os11g18700.1	upstream_gene_variant ; 2309.0bp to feature; MODIFIER	silent_mutation	Average:12.309; most accessible tissue: Zhenshan97 flag leaf, score: 18.943	N	N	N	N
vg1110586892	G -> A	LOC_Os11g18690-LOC_Os11g18700	intergenic_region ; MODIFIER	silent_mutation	Average:12.309; most accessible tissue: Zhenshan97 flag leaf, score: 18.943	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110586892	NA	1.61E-06	mr1580	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
vg1110586892	NA	4.11E-08	mr1825	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