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Detailed information for vg1113418649:

Variant ID: vg1113418649 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13418649
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGTTCATGTACTAAAACGCACCTACTTGTCAAGTTGTTGTACTCGGATGATCAATTCTCAAGTTCTTGCACTATATCGCACCCACATGCCAAGTTATT[G/A]
TACCGTAGGTGCAATTTACACTTCTAAATAAAATCGGTACCTATAGTATTAGTTCCCTTTATTTTTTAAAAAAATGACACTAAATATTAATATATAAGGT

Reverse complement sequence

ACCTTATATATTAATATTTAGTGTCATTTTTTTAAAAAATAAAGGGAACTAATACTATAGGTACCGATTTTATTTAGAAGTGTAAATTGCACCTACGGTA[C/T]
AATAACTTGGCATGTGGGTGCGATATAGTGCAAGAACTTGAGAATTGATCATCCGAGTACAACAACTTGACAAGTAGGTGCGTTTTAGTACATGAACTTC

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	98.50%	1.00%	0.55%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	96.60%	1.90%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	96.00%	1.40%	2.61%	0.00%	NA
Tropical Japonica	504	96.40%	3.00%	0.60%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	15.60%	1.04%	0.00%	NA
Intermediate	90	96.70%	2.20%	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
vg1113418649	G -> A	LOC_Os11g23736.1	upstream_gene_variant ; 3286.0bp to feature; MODIFIER	silent_mutation	Average:37.598; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg1113418649	G -> A	LOC_Os11g23740.1	upstream_gene_variant ; 152.0bp to feature; MODIFIER	silent_mutation	Average:37.598; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N
vg1113418649	G -> A	LOC_Os11g23736-LOC_Os11g23740	intergenic_region ; MODIFIER	silent_mutation	Average:37.598; most accessible tissue: Zhenshan97 young leaf, score: 65.28	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113418649	5.29E-07	5.29E-07	mr1193_2	Jap_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