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Detailed information for vg0823149834:

Variant ID: vg0823149834 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 23149834
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGAATCCATATAAGAACCCAATACTAGATTAATTAAAACTCAAAAAAATAATATCCAAAATTAGAAAAATTAAAAGAGAGTTCAAGTAGTAATACAATT[T/C]
TGAAACAACTGAAATTCAAAAATAAAAAATAAAAATATTAAAAAAACACTATACAATTTATAAATAACTAAAATTGGTGATAAAAATAAAGATTATTGAA

Reverse complement sequence

TTCAATAATCTTTATTTTTATCACCAATTTTAGTTATTTATAAATTGTATAGTGTTTTTTTAATATTTTTATTTTTTATTTTTGAATTTCAGTTGTTTCA[A/G]
AATTGTATTACTACTTGAACTCTCTTTTAATTTTTCTAATTTTGGATATTATTTTTTTGAGTTTTAATTAATCTAGTATTGGGTTCTTATATGGATTCTT

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 65.40% 34.20% 0.36% 0.00% NA
All Indica  2759 96.80% 2.80% 0.43% 0.00% NA
All Japonica  1512 1.40% 98.40% 0.20% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 97.80% 1.30% 0.86% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.00% 0.51% 0.00% NA
Temperate Japonica  767 1.60% 98.20% 0.26% 0.00% NA
Tropical Japonica  504 0.60% 99.20% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 57.80% 40.00% 2.22% 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
vg0823149834 T -> C LOC_Os08g36670.1 upstream_gene_variant ; 4997.0bp to feature; MODIFIER silent_mutation Average:18.412; most accessible tissue: Zhenshan97 young leaf, score: 24.604 N N N N
vg0823149834 T -> C LOC_Os08g36680.1 intron_variant ; MODIFIER silent_mutation Average:18.412; most accessible tissue: Zhenshan97 young leaf, score: 24.604 N N N N
vg0823149834 T -> C LOC_Os08g36680.2 intron_variant ; MODIFIER silent_mutation Average:18.412; most accessible tissue: Zhenshan97 young leaf, score: 24.604 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0823149834 6.78E-06 NA mr1004 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
vg0823149834 NA 1.24E-10 mr1005 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
vg0823149834 7.99E-07 NA mr1011 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
vg0823149834 4.93E-07 NA mr1011 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
vg0823149834 9.05E-06 NA mr1012 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
vg0823149834 NA 2.14E-32 mr1243 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
vg0823149834 NA 1.49E-08 mr1806 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
vg0823149834 NA 2.98E-20 mr1838 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
vg0823149834 NA 4.59E-07 mr1915 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
vg0823149834 NA 1.42E-33 mr1932 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
vg0823149834 NA 2.21E-16 mr1968 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
vg0823149834 NA 5.74E-19 mr1276_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
vg0823149834 NA 1.14E-17 mr1682_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
vg0823149834 NA 5.96E-10 mr1806_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
vg0823149834 NA 6.68E-22 mr1968_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