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Detailed information for vg0217651623:

Variant ID: vg0217651623 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17651623
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TATCATTTATAGATTTAACTGCGATTTATTTATCAAATCAACTGGCACGCTCATACATTCGAAGGCGAGCTTTGGACCTGCACTGGAGTTAAGCAGATCT[C/T]
CCAGGCCTTGTGTTTTCTGTCAACACGCTTTTGGCACACCTGGTGGGACATTTAAGAAGTCAGCCAACAATTCTTCCTCATGGCCGAGAAACCACCACCA

Reverse complement sequence

TGGTGGTGGTTTCTCGGCCATGAGGAAGAATTGTTGGCTGACTTCTTAAATGTCCCACCAGGTGTGCCAAAAGCGTGTTGACAGAAAACACAAGGCCTGG[G/A]
AGATCTGCTTAACTCCAGTGCAGGTCCAAAGCTCGCCTTCGAATGTATGAGCGTGCCAGTTGATTTGATAAATAAATCGCAGTTAAATCTATAAATGATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.90%	27.50%	3.79%	0.78%	NA
All Indica	2759	47.50%	45.80%	5.76%	0.91%	NA
All Japonica	1512	98.70%	0.70%	0.46%	0.20%	NA
Aus	269	97.80%	1.50%	0.74%	0.00%	NA
Indica I	595	38.50%	52.10%	7.73%	1.68%	NA
Indica II	465	23.40%	67.70%	7.53%	1.29%	NA
Indica III	913	68.70%	28.60%	2.63%	0.11%	NA
Indica Intermediate	786	44.00%	48.10%	6.87%	1.02%	NA
Temperate Japonica	767	98.80%	0.70%	0.39%	0.13%	NA
Tropical Japonica	504	98.60%	0.40%	0.79%	0.20%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	85.40%	4.20%	4.17%	6.25%	NA
Intermediate	90	68.90%	20.00%	7.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217651623	C -> T	LOC_Os02g29650.1	upstream_gene_variant ; 80.0bp to feature; MODIFIER	silent_mutation	Average:27.654; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0217651623	C -> T	LOC_Os02g29640-LOC_Os02g29650	intergenic_region ; MODIFIER	silent_mutation	Average:27.654; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0217651623	C -> DEL	N	N	silent_mutation	Average:27.654; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217651623	NA	1.04E-14	mr1013	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
vg0217651623	NA	1.43E-09	mr1013	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
vg0217651623	NA	3.73E-09	mr1014	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
vg0217651623	3.67E-06	8.94E-11	mr1015	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
vg0217651623	NA	4.72E-15	mr1031	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
vg0217651623	NA	2.86E-09	mr1031	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
vg0217651623	NA	8.29E-14	mr1034	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
vg0217651623	NA	2.89E-09	mr1034	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
vg0217651623	NA	2.87E-14	mr1056	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
vg0217651623	NA	3.51E-08	mr1056	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
vg0217651623	NA	3.81E-06	mr1268	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
vg0217651623	NA	6.91E-06	mr1677	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
vg0217651623	NA	3.72E-10	mr1720	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
vg0217651623	NA	1.10E-09	mr1319_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
vg0217651623	NA	7.40E-07	mr1428_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