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Detailed information for vg0217651623:

Variant ID: vg0217651623 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17651623
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary 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 SizeFrequency 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