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Detailed information for vg1125091275:

Variant ID: vg1125091275 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25091275
Reference Allele: A	Alternative Allele: G,C
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAACTGAGTGCAATAAAAACTTCCGTTATCTTAAAGAAAATCAATGACACCAGATACACCTACCGATACATATGCAAAAGTTGTTATTGTATCTACT[A/G,C]
CGCCTTCTCCTTTAAATACATTTTATTTATTTTCGCGCAACGTTCCATTGCATTCTGAGAAATTAATATCCAAACTATTCTTGTGATATATACTTCCTCC

Reverse complement sequence

GGAGGAAGTATATATCACAAGAATAGTTTGGATATTAATTTCTCAGAATGCAATGGAACGTTGCGCGAAAATAAATAAAATGTATTTAAAGGAGAAGGCG[T/C,G]
AGTAGATACAATAACAACTTTTGCATATGTATCGGTAGGTGTATCTGGTGTCATTGATTTTCTTTAAGATAACGGAAGTTTTTATTGCACTCAGTTAATT

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	92.80%	6.90%	0.28%	0.00%	C: 0.02%
All Indica	2759	99.30%	0.30%	0.43%	0.00%	NA
All Japonica	1512	81.70%	18.30%	0.07%	0.00%	NA
Aus	269	85.90%	14.10%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.50%	0.20%	0.33%	0.00%	NA
Indica Intermediate	786	98.20%	0.60%	1.15%	0.00%	NA
Temperate Japonica	767	91.30%	8.60%	0.13%	0.00%	NA
Tropical Japonica	504	71.60%	28.40%	0.00%	0.00%	NA
Japonica Intermediate	241	72.20%	27.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	0.00%	C: 1.04%
Intermediate	90	95.60%	4.40%	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
vg1125091275	A -> G	LOC_Os11g41760-LOC_Os11g41770	intergenic_region ; MODIFIER	silent_mutation	Average:52.632; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg1125091275	A -> C	LOC_Os11g41760-LOC_Os11g41770	intergenic_region ; MODIFIER	silent_mutation	Average:52.632; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125091275	2.58E-10	NA	mr1238	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
vg1125091275	NA	5.04E-07	mr1238	Jap_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
vg1125091275	9.16E-08	NA	mr1309	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
vg1125091275	NA	5.71E-06	mr1309	Jap_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
vg1125091275	7.91E-08	NA	mr1484	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
vg1125091275	7.98E-06	1.14E-06	mr1484	Jap_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
vg1125091275	NA	2.26E-07	mr1723	Jap_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
vg1125091275	3.36E-08	NA	mr1841	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
vg1125091275	NA	1.11E-06	mr1841	Jap_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
vg1125091275	4.83E-09	2.26E-16	mr1900	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
vg1125091275	NA	3.54E-08	mr1900	Jap_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
vg1125091275	1.32E-06	NA	mr1925	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
vg1125091275	NA	3.69E-06	mr1063_2	Jap_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
vg1125091275	3.57E-10	NA	mr1238_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
vg1125091275	6.61E-09	NA	mr1484_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
vg1125091275	NA	2.99E-06	mr1723_2	Jap_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
vg1125091275	1.42E-08	NA	mr1841_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
vg1125091275	1.01E-08	NA	mr1900_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
vg1125091275	3.28E-08	3.61E-07	mr1925_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
vg1125091275	4.18E-07	NA	mr1945_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