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Detailed information for vg0204657133:

Variant ID: vg0204657133 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4657133
Reference Allele: A	Alternative Allele: G
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: 119. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTTGATAGGAATATAAGTGTAAAACAGATGATTGCAAAACGCAGGAAAAACACAGGAATGATCGTTTGATTGAACTACTGGAAAAACACAGGAATTG[A/G]
ATGAGAGATATAGACTCAAAGGAAATTTAGCAAGAGGTTGAAGCTCTTGCTAAATTTCCTCCAAAATCTCTATAGGATTGTCCATTCCATAGGAATGATT

Reverse complement sequence

AATCATTCCTATGGAATGGACAATCCTATAGAGATTTTGGAGGAAATTTAGCAAGAGCTTCAACCTCTTGCTAAATTTCCTTTGAGTCTATATCTCTCAT[T/C]
CAATTCCTGTGTTTTTCCAGTAGTTCAATCAAACGATCATTCCTGTGTTTTTCCTGCGTTTTGCAATCATCTGTTTTACACTTATATTCCTATCAAAATC

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	82.10%	17.20%	0.66%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.04%	0.00%	NA
All Japonica	1512	46.60%	51.70%	1.79%	0.00%	NA
Aus	269	98.10%	1.50%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	10.70%	86.70%	2.61%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	64.30%	32.80%	2.90%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	20.00%	2.22%	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
vg0204657133	A -> G	LOC_Os02g09080.1	downstream_gene_variant ; 3150.0bp to feature; MODIFIER	silent_mutation	Average:33.165; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0204657133	A -> G	LOC_Os02g09090.1	downstream_gene_variant ; 716.0bp to feature; MODIFIER	silent_mutation	Average:33.165; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0204657133	A -> G	LOC_Os02g09100.1	downstream_gene_variant ; 1003.0bp to feature; MODIFIER	silent_mutation	Average:33.165; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0204657133	A -> G	LOC_Os02g09090-LOC_Os02g09100	intergenic_region ; MODIFIER	silent_mutation	Average:33.165; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204657133	5.28E-07	NA	mr1549	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
vg0204657133	NA	7.22E-07	mr1668	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
vg0204657133	NA	4.93E-10	mr1712	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
vg0204657133	8.43E-09	NA	mr1757	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
vg0204657133	NA	4.11E-06	mr1977	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
vg0204657133	5.86E-07	NA	mr1549_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