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Detailed information for vg0201373773:

Variant ID: vg0201373773 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 1373773
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CTTAAGATCCTTCAAGCCAGGAGTACGATATTACACCTCTGGGTAGCCCGAACCTTTACAATTCTTTGTGTTCATCTATTATTGCGCTCCAATGGGGCTC[A/G]
AACTCCTCACTCATATGCGACTAGCTCCCCAACTGAACTGACCGAAAGGGTCCCATTGGATCCCCACCATCGAGGTCCATACCCTAACAATATTTGTCTC

Reverse complement sequence

GAGACAAATATTGTTAGGGTATGGACCTCGATGGTGGGGATCCAATGGGACCCTTTCGGTCAGTTCAGTTGGGGAGCTAGTCGCATATGAGTGAGGAGTT[T/C]
GAGCCCCATTGGAGCGCAATAATAGATGAACACAAAGAATTGTAAAGGTTCGGGCTACCCAGAGGTGTAATATCGTACTCCTGGCTTGAAGGATCTTAAG

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	78.50%	21.40%	0.13%	0.00%	NA
All Indica	2759	70.30%	29.50%	0.22%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	31.20%	68.80%	0.00%	0.00%	NA
Indica I	595	94.80%	5.00%	0.17%	0.00%	NA
Indica II	465	86.90%	12.90%	0.22%	0.00%	NA
Indica III	913	41.30%	58.60%	0.11%	0.00%	NA
Indica Intermediate	786	75.60%	24.00%	0.38%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0201373773	A -> G	LOC_Os02g03390.1	upstream_gene_variant ; 1912.0bp to feature; MODIFIER	silent_mutation	Average:61.659; most accessible tissue: Callus, score: 80.733	N	N	N	N
vg0201373773	A -> G	LOC_Os02g03370.1	downstream_gene_variant ; 4734.0bp to feature; MODIFIER	silent_mutation	Average:61.659; most accessible tissue: Callus, score: 80.733	N	N	N	N
vg0201373773	A -> G	LOC_Os02g03380.1	intron_variant ; MODIFIER	silent_mutation	Average:61.659; most accessible tissue: Callus, score: 80.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0201373773	NA	3.68E-06	mr1004	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
vg0201373773	4.26E-06	NA	mr1842	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