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Detailed information for vg0219817547:

Variant ID: vg0219817547 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 19817547
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, G: 0.41, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TGTCCAAGATCATATGCTGACTGTACATTCATGCTTTTTTTTTATACATAACTGGACATTCATACTTACTATGTTTCATTTACGCATAGTACTTTATTGC[A/G]
CGAGCAATTTTGAAGTCCTTGTGGAGGTACCACTTTTTCTATTATAAATTTGGTACCTCATAGTACACTAAATTTTTTATACCTCATGATATCTCCTTAA

Reverse complement sequence

TTAAGGAGATATCATGAGGTATAAAAAATTTAGTGTACTATGAGGTACCAAATTTATAATAGAAAAAGTGGTACCTCCACAAGGACTTCAAAATTGCTCG[T/C]
GCAATAAAGTACTATGCGTAAATGAAACATAGTAAGTATGAATGTCCAGTTATGTATAAAAAAAAAGCATGAATGTACAGTCAGCATATGATCTTGGACA

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	52.30%	47.10%	0.08%	0.51%	NA
All Indica	2759	85.80%	13.50%	0.11%	0.54%	NA
All Japonica	1512	1.70%	98.00%	0.00%	0.26%	NA
Aus	269	18.60%	81.40%	0.00%	0.00%	NA
Indica I	595	81.50%	17.50%	0.17%	0.84%	NA
Indica II	465	83.00%	16.30%	0.22%	0.43%	NA
Indica III	913	92.90%	6.90%	0.00%	0.22%	NA
Indica Intermediate	786	82.60%	16.50%	0.13%	0.76%	NA
Temperate Japonica	767	1.20%	98.40%	0.00%	0.39%	NA
Tropical Japonica	504	1.60%	98.20%	0.00%	0.20%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	33.30%	60.00%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0219817547	A -> G	LOC_Os02g33360.1	upstream_gene_variant ; 3141.0bp to feature; MODIFIER	silent_mutation	Average:51.418; most accessible tissue: Callus, score: 85.372	N	N	N	N
vg0219817547	A -> G	LOC_Os02g33340-LOC_Os02g33360	intergenic_region ; MODIFIER	silent_mutation	Average:51.418; most accessible tissue: Callus, score: 85.372	N	N	N	N
vg0219817547	A -> DEL	N	N	silent_mutation	Average:51.418; most accessible tissue: Callus, score: 85.372	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0219817547	NA	7.69E-10	mr1151	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
vg0219817547	NA	3.67E-13	mr1183	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
vg0219817547	NA	2.85E-31	mr1225	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
vg0219817547	NA	6.87E-18	mr1255	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
vg0219817547	NA	6.60E-13	mr1503	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
vg0219817547	NA	3.96E-06	mr1881	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
vg0219817547	NA	1.44E-12	mr1138_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
vg0219817547	NA	4.17E-33	mr1161_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
vg0219817547	NA	1.11E-20	mr1164_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
vg0219817547	NA	1.44E-09	mr1172_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
vg0219817547	NA	2.33E-17	mr1180_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
vg0219817547	NA	1.33E-06	mr1180_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
vg0219817547	NA	3.46E-20	mr1183_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
vg0219817547	NA	7.24E-06	mr1519_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
vg0219817547	3.98E-07	NA	mr1707_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
vg0219817547	3.33E-06	NA	mr1707_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
vg0219817547	NA	6.50E-09	mr1851_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
vg0219817547	3.58E-06	NA	mr1860_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
vg0219817547	1.42E-06	NA	mr1860_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