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Detailed information for vg1115243061:

Variant ID: vg1115243061 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 15243061
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTTTTAATTCTGAATTTTTATTTGTCTTCCGAATATTAACTAAAATCGTATTGAGTTCTTATATTAACTCTTCTCTCAATATTTCTTATTTTTAATT[C/T]
CGAATTTCAGCTATTTTTGAATTGTATTTCTACTTGGACTCTCCTTTTCTTTTTCTCTGATTAATGTGGGAATTTCTAGCCCCCACAGTGAACGTGGTGC

Reverse complement sequence

GCACCACGTTCACTGTGGGGGCTAGAAATTCCCACATTAATCAGAGAAAAAGAAAAGGAGAGTCCAAGTAGAAATACAATTCAAAAATAGCTGAAATTCG[G/A]
AATTAAAAATAAGAAATATTGAGAGAAGAGTTAATATAAGAACTCAATACGATTTTAGTTAATATTCGGAAGACAAATAAAAATTCAGAATTAAAAATAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.80%	35.00%	1.12%	2.07%	NA
All Indica	2759	92.50%	2.40%	1.59%	3.48%	NA
All Japonica	1512	3.10%	96.80%	0.07%	0.07%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	92.10%	3.50%	2.35%	2.02%	NA
Indica II	465	87.30%	1.10%	2.15%	9.46%	NA
Indica III	913	98.20%	0.40%	0.00%	1.31%	NA
Indica Intermediate	786	89.30%	4.60%	2.54%	3.56%	NA
Temperate Japonica	767	3.30%	96.60%	0.00%	0.13%	NA
Tropical Japonica	504	3.40%	96.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	9.40%	86.50%	4.17%	0.00%	NA
Intermediate	90	50.00%	44.40%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1115243061	C -> T	LOC_Os11g26594.1	downstream_gene_variant ; 3771.0bp to feature; MODIFIER	silent_mutation	Average:23.301; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1115243061	C -> T	LOC_Os11g26600.1	downstream_gene_variant ; 921.0bp to feature; MODIFIER	silent_mutation	Average:23.301; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1115243061	C -> T	LOC_Os11g26594.2	downstream_gene_variant ; 3793.0bp to feature; MODIFIER	silent_mutation	Average:23.301; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1115243061	C -> T	LOC_Os11g26594-LOC_Os11g26600	intergenic_region ; MODIFIER	silent_mutation	Average:23.301; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1115243061	C -> DEL	N	N	silent_mutation	Average:23.301; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1115243061	NA	1.84E-06	mr1424	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
vg1115243061	NA	8.39E-14	mr1874	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
vg1115243061	NA	2.21E-10	mr1904	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
vg1115243061	NA	2.60E-10	mr1835_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
vg1115243061	4.66E-06	8.26E-16	mr1904_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