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Detailed information for vg1116521139:

Variant ID: vg1116521139 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16521139
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CGTATACCAATTGTAAAGGGTCATTCCCACCCCAAAAGCTAGCCATTGAGGTGAGGGGCCCCCACTTATATCTTAGGTTCTCTGCTCTTCCACAACCAAT[G/A]
TGGGATTATTCAACAGCCTCTTATGAAGTAAAACCGTAGCAAAGTAGCAAATAAAAAAAAGTATGAAGTTTGCGAATCCAAATTAGAATTTCACAATATA

Reverse complement sequence

TATATTGTGAAATTCTAATTTGGATTCGCAAACTTCATACTTTTTTTTATTTGCTACTTTGCTACGGTTTTACTTCATAAGAGGCTGTTGAATAATCCCA[C/T]
ATTGGTTGTGGAAGAGCAGAGAACCTAAGATATAAGTGGGGGCCCCTCACCTCAATGGCTAGCTTTTGGGGTGGGAATGACCCTTTACAATTGGTATACG

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	53.60%	46.30%	0.13%	0.02%	NA
All Indica	2759	79.70%	20.20%	0.14%	0.04%	NA
All Japonica	1512	1.70%	98.30%	0.07%	0.00%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	88.10%	11.90%	0.00%	0.00%	NA
Indica II	465	91.60%	8.20%	0.22%	0.00%	NA
Indica III	913	68.50%	31.30%	0.11%	0.11%	NA
Indica Intermediate	786	79.30%	20.50%	0.25%	0.00%	NA
Temperate Japonica	767	1.70%	98.30%	0.00%	0.00%	NA
Tropical Japonica	504	1.60%	98.20%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	53.30%	45.60%	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
vg1116521139	G -> A	LOC_Os11g28610-LOC_Os11g28628	intergenic_region ; MODIFIER	silent_mutation	Average:39.111; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N
vg1116521139	G -> DEL	N	N	silent_mutation	Average:39.111; most accessible tissue: Zhenshan97 root, score: 55.432	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116521139	NA	1.85E-08	mr1342	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
vg1116521139	NA	3.92E-09	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
vg1116521139	2.32E-07	NA	mr1873	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
vg1116521139	NA	5.17E-12	mr1216_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
vg1116521139	NA	1.35E-07	mr1335_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
vg1116521139	NA	7.67E-08	mr1378_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