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Detailed information for vg0621502460:

Variant ID: vg0621502460 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21502460
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCAATGTGTACGGATGCACGTATATACGTAACAACTCTGTACGCTCCTATTTCCATTCTTCTCTTTTCATTCTATTATCTATTTATCTCTCCTATTTT[G/A]
CTTCTTCTAATAGAAAGCAAAATTTATGTAAAAACATTTAGGCAACTATTACATTTAAATCATAAAAGTATTCTAATATGCTTATGCTGTTAGACTATTT

Reverse complement sequence

AAATAGTCTAACAGCATAAGCATATTAGAATACTTTTATGATTTAAATGTAATAGTTGCCTAAATGTTTTTACATAAATTTTGCTTTCTATTAGAAGAAG[C/T]
AAAATAGGAGAGATAAATAGATAATAGAATGAAAAGAGAAGAATGGAAATAGGAGCGTACAGAGTTGTTACGTATATACGTGCATCCGTACACATTGAGT

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	80.20%	19.80%	0.02%	0.00%	NA
All Indica	2759	94.90%	5.10%	0.00%	0.00%	NA
All Japonica	1512	67.60%	32.30%	0.07%	0.00%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	97.80%	2.20%	0.00%	0.00%	NA
Indica III	913	90.40%	9.60%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	5.50%	0.00%	0.00%	NA
Temperate Japonica	767	58.80%	41.10%	0.13%	0.00%	NA
Tropical Japonica	504	85.50%	14.50%	0.00%	0.00%	NA
Japonica Intermediate	241	58.10%	41.90%	0.00%	0.00%	NA
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0621502460	G -> A	LOC_Os06g36600.1	upstream_gene_variant ; 4828.0bp to feature; MODIFIER	silent_mutation	Average:51.291; most accessible tissue: Callus, score: 78.0	N	N	N	N
vg0621502460	G -> A	LOC_Os06g36590.1	downstream_gene_variant ; 1086.0bp to feature; MODIFIER	silent_mutation	Average:51.291; most accessible tissue: Callus, score: 78.0	N	N	N	N
vg0621502460	G -> A	LOC_Os06g36590-LOC_Os06g36600	intergenic_region ; MODIFIER	silent_mutation	Average:51.291; most accessible tissue: Callus, score: 78.0	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621502460	NA	2.70E-13	mr1465	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