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Detailed information for vg0512660263:

Variant ID: vg0512660263 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12660263
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

GGTAACCTCCTAAAACTAACTTACACAAAAAATTTTTGGTATTTAATTTTTTTTGTGGTTTTCATTTAAAAATATATCTTAGTAAATTGAGGTATTTCCA[G/C]
ATTGGATTTTATTTTTGAATTTTAAACCTTATTTCGACTAAAATTTCTTTATTCAATTTATTTGAAAACTTCTTTTACTTTATTGATTATGGTCCAAGAA

Reverse complement sequence

TTCTTGGACCATAATCAATAAAGTAAAAGAAGTTTTCAAATAAATTGAATAAAGAAATTTTAGTCGAAATAAGGTTTAAAATTCAAAAATAAAATCCAAT[C/G]
TGGAAATACCTCAATTTACTAAGATATATTTTTAAATGAAAACCACAAAAAAAATTAAATACCAAAAATTTTTTGTGTAAGTTAGTTTTAGGAGGTTACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.80%	2.80%	0.49%	0.00%	NA
All Indica	2759	94.50%	4.70%	0.83%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.90%	6.90%	2.18%	0.00%	NA
Indica II	465	93.80%	5.80%	0.43%	0.00%	NA
Indica III	913	97.70%	2.20%	0.11%	0.00%	NA
Indica Intermediate	786	93.90%	5.20%	0.89%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	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	98.90%	1.10%	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
vg0512660263	G -> C	LOC_Os05g22350.1	upstream_gene_variant ; 1947.0bp to feature; MODIFIER	silent_mutation	Average:31.252; most accessible tissue: Callus, score: 75.899	N	N	N	N
vg0512660263	G -> C	LOC_Os05g22360.1	downstream_gene_variant ; 3903.0bp to feature; MODIFIER	silent_mutation	Average:31.252; most accessible tissue: Callus, score: 75.899	N	N	N	N
vg0512660263	G -> C	LOC_Os05g22350-LOC_Os05g22360	intergenic_region ; MODIFIER	silent_mutation	Average:31.252; most accessible tissue: Callus, score: 75.899	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512660263	3.40E-07	8.26E-13	mr1023_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