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Detailed information for vg1126386642:

Variant ID: vg1126386642 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26386642
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, G: 0.22, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

GATATATAACTTGTTGAACAGTGCTTGCTACTCCAAGATCTTGTGTGATTTTGCTCTATGGGCGCTTGTGATGTTGATAGATTTGCTTGAGATTTCCACA[G/C]
GGGGTTTTTTCTTCTTCTTTTGGAGGCTCCAAATTAGAAGATGCATGCACTTTGATGAAAACTACTCTAGCTATCCAAAGCTACAAACTGATTTGATCTT

Reverse complement sequence

AAGATCAAATCAGTTTGTAGCTTTGGATAGCTAGAGTAGTTTTCATCAAAGTGCATGCATCTTCTAATTTGGAGCCTCCAAAAGAAGAAGAAAAAACCCC[C/G]
TGTGGAAATCTCAAGCAAATCTATCAACATCACAAGCGCCCATAGAGCAAAATCACACAAGATCTTGGAGTAGCAAGCACTGTTCAACAAGTTATATATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.00%	33.10%	0.23%	1.63%	NA
All Indica	2759	63.80%	35.60%	0.22%	0.40%	NA
All Japonica	1512	68.40%	27.70%	0.07%	3.84%	NA
Aus	269	46.10%	50.60%	1.12%	2.23%	NA
Indica I	595	80.50%	19.50%	0.00%	0.00%	NA
Indica II	465	85.60%	14.20%	0.22%	0.00%	NA
Indica III	913	46.90%	52.50%	0.22%	0.44%	NA
Indica Intermediate	786	57.90%	40.80%	0.38%	0.89%	NA
Temperate Japonica	767	57.50%	41.90%	0.00%	0.65%	NA
Tropical Japonica	504	80.60%	12.10%	0.00%	7.34%	NA
Japonica Intermediate	241	77.60%	15.40%	0.41%	6.64%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	28.90%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126386642	G -> DEL	N	N	silent_mutation	Average:50.771; most accessible tissue: Zhenshan97 flower, score: 68.001	N	N	N	N
vg1126386642	G -> C	LOC_Os11g43700-LOC_Os11g43710	intergenic_region ; MODIFIER	silent_mutation	Average:50.771; most accessible tissue: Zhenshan97 flower, score: 68.001	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126386642	NA	7.54E-06	mr1616	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
vg1126386642	3.41E-07	2.25E-09	mr1662	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
vg1126386642	1.51E-10	8.31E-13	mr1662_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