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Detailed information for vg0222574285:

Variant ID: vg0222574285 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22574285
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACCTTAAGATACTTATTATTACCTCCGTTTTAGGTTATAAGAAGATTCATTAACATCTATATGAATGTGGGCAATGCTAGAAAGTCTTATAATATGAAAC[G/A]
GAGGAAGTAGTACATAGAGATACCAAATTTTACACTAAAAAATATGGTACCTCTAGATACCTTCTCAAGAATAGTAAAATTACCCTACTAACAATAGAGA

Reverse complement sequence

TCTCTATTGTTAGTAGGGTAATTTTACTATTCTTGAGAAGGTATCTAGAGGTACCATATTTTTTAGTGTAAAATTTGGTATCTCTATGTACTACTTCCTC[C/T]
GTTTCATATTATAAGACTTTCTAGCATTGCCCACATTCATATAGATGTTAATGAATCTTCTTATAACCTAAAACGGAGGTAATAATAAGTATCTTAAGGT

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	53.60%	46.00%	0.34%	0.00%	NA
All Indica	2759	84.90%	14.50%	0.54%	0.00%	NA
All Japonica	1512	4.00%	96.00%	0.00%	0.00%	NA
Aus	269	37.20%	62.80%	0.00%	0.00%	NA
Indica I	595	78.80%	19.70%	1.51%	0.00%	NA
Indica II	465	93.30%	6.50%	0.22%	0.00%	NA
Indica III	913	84.90%	14.90%	0.22%	0.00%	NA
Indica Intermediate	786	84.60%	15.00%	0.38%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	9.90%	90.10%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	32.20%	66.70%	1.11%	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
vg0222574285	G -> A	LOC_Os02g37360.1	upstream_gene_variant ; 944.0bp to feature; MODIFIER	silent_mutation	Average:37.843; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0222574285	G -> A	LOC_Os02g37350.1	downstream_gene_variant ; 2757.0bp to feature; MODIFIER	silent_mutation	Average:37.843; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0222574285	G -> A	LOC_Os02g37380.1	downstream_gene_variant ; 4875.0bp to feature; MODIFIER	silent_mutation	Average:37.843; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg0222574285	G -> A	LOC_Os02g37360-LOC_Os02g37380	intergenic_region ; MODIFIER	silent_mutation	Average:37.843; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222574285	NA	1.46E-39	mr1124	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
vg0222574285	1.52E-06	1.27E-12	mr1188	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
vg0222574285	NA	3.05E-15	mr1592	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
vg0222574285	1.37E-06	NA	mr1067_2	Ind_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
vg0222574285	1.47E-06	2.75E-13	mr1188_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