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Detailed information for vg0217266536:

Variant ID: vg0217266536 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17266536
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGACAGTTCAAACGTACACATTCTTGTGTATCAAGTTTCATTAGCCTATATGACATTTTAAATAGAGTTAAACTCAAATAAAACATGCATTGATAATGG[G/A]
ACAATATAAACAGGAAAGCGATGTAAAAATAATAAAAAGCAAAAGTACGAATTAATTAGTTAATTCATAAAAATGCAAAATAGGAAGGGGTTTGATATGG

Reverse complement sequence

CCATATCAAACCCCTTCCTATTTTGCATTTTTATGAATTAACTAATTAATTCGTACTTTTGCTTTTTATTATTTTTACATCGCTTTCCTGTTTATATTGT[C/T]
CCATTATCAATGCATGTTTTATTTGAGTTTAACTCTATTTAAAATGTCATATAGGCTAATGAAACTTGATACACAAGAATGTGTACGTTTGAACTGTCTT

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	66.40%	15.60%	2.77%	15.26%	NA
All Indica	2759	50.60%	22.80%	4.64%	22.04%	NA
All Japonica	1512	97.90%	0.50%	0.00%	1.59%	NA
Aus	269	69.50%	1.50%	0.37%	28.62%	NA
Indica I	595	64.70%	3.90%	9.08%	22.35%	NA
Indica II	465	83.00%	7.70%	2.15%	7.10%	NA
Indica III	913	20.40%	46.20%	2.85%	30.56%	NA
Indica Intermediate	786	55.70%	18.70%	4.83%	20.74%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	95.20%	0.60%	0.00%	4.17%	NA
Japonica Intermediate	241	97.50%	2.10%	0.00%	0.41%	NA
VI/Aromatic	96	13.50%	85.40%	0.00%	1.04%	NA
Intermediate	90	71.10%	14.40%	2.22%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217266536	G -> A	LOC_Os02g29140.1	upstream_gene_variant ; 470.0bp to feature; MODIFIER	silent_mutation	Average:62.862; most accessible tissue: Callus, score: 92.518	N	N	N	N
vg0217266536	G -> A	LOC_Os02g29150.2	downstream_gene_variant ; 4647.0bp to feature; MODIFIER	silent_mutation	Average:62.862; most accessible tissue: Callus, score: 92.518	N	N	N	N
vg0217266536	G -> A	LOC_Os02g29140-LOC_Os02g29150	intergenic_region ; MODIFIER	silent_mutation	Average:62.862; most accessible tissue: Callus, score: 92.518	N	N	N	N
vg0217266536	G -> DEL	N	N	silent_mutation	Average:62.862; most accessible tissue: Callus, score: 92.518	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217266536	2.43E-07	NA	mr1109	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
vg0217266536	4.02E-10	NA	mr1129	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
vg0217266536	4.42E-07	2.70E-06	mr1129	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
vg0217266536	2.32E-06	NA	mr1235	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
vg0217266536	5.60E-08	NA	mr1251	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
vg0217266536	2.27E-07	6.33E-19	mr1253	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
vg0217266536	9.39E-06	NA	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
vg0217266536	1.95E-09	NA	mr1257	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
vg0217266536	7.72E-06	NA	mr1257	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
vg0217266536	NA	2.35E-07	mr1377	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
vg0217266536	1.19E-07	NA	mr1423	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
vg0217266536	NA	8.37E-06	mr1423	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
vg0217266536	9.44E-08	NA	mr1435	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
vg0217266536	5.49E-06	NA	mr1599	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
vg0217266536	1.68E-06	NA	mr1089_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
vg0217266536	3.82E-06	NA	mr1093_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
vg0217266536	6.87E-07	NA	mr1109_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
vg0217266536	8.51E-06	NA	mr1109_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
vg0217266536	6.44E-08	NA	mr1129_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
vg0217266536	1.68E-06	NA	mr1129_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
vg0217266536	2.35E-07	NA	mr1251_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
vg0217266536	2.45E-06	NA	mr1251_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
vg0217266536	1.65E-08	NA	mr1253_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
vg0217266536	2.24E-06	2.19E-06	mr1253_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
vg0217266536	2.90E-08	NA	mr1255_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
vg0217266536	1.45E-06	2.14E-06	mr1255_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
vg0217266536	1.00E-08	NA	mr1257_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
vg0217266536	1.49E-06	NA	mr1257_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
vg0217266536	3.56E-06	NA	mr1423_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
vg0217266536	2.73E-07	NA	mr1435_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
vg0217266536	2.90E-06	NA	mr1435_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
vg0217266536	2.81E-06	NA	mr1599_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