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Detailed information for vg0517887151:

Variant ID: vg0517887151 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17887151
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


ACATCTATTATCTGACATGAAAAATAGAAGATAAAAAGATGTGGTAATTATACTTACTCAGGATCTTGGTACACACTACTACTGAACCCATGAGATGGGC[T/C]
GACGTCTTCGTATCCTCTAAGTAACCTAACAAGTCCAGCATCAGCCACCTTTGCAATGAAATTTTCATCAACCAACACATTGCTTGTCTTGAAATCCTTG

Reverse complement sequence

CAAGGATTTCAAGACAAGCAATGTGTTGGTTGATGAAAATTTCATTGCAAAGGTGGCTGATGCTGGACTTGTTAGGTTACTTAGAGGATACGAAGACGTC[A/G]
GCCCATCTCATGGGTTCAGTAGTAGTGTGTACCAAGATCCTGAGTAAGTATAATTACCACATCTTTTTATCTTCTATTTTTCATGTCAGATAATAGATGT

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 64.70% 35.00% 0.25% 0.00% NA
All Indica  2759 94.10% 5.60% 0.25% 0.00% NA
All Japonica  1512 8.70% 91.10% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 74.40% 25.20% 0.43% 0.00% NA
Indica III  913 99.10% 0.50% 0.33% 0.00% NA
Indica Intermediate  786 95.50% 4.20% 0.25% 0.00% NA
Temperate Japonica  767 3.00% 97.00% 0.00% 0.00% NA
Tropical Japonica  504 20.20% 79.60% 0.20% 0.00% NA
Japonica Intermediate  241 2.90% 96.70% 0.41% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 56.70% 40.00% 3.33% 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
vg0517887151 T -> C LOC_Os05g30820.1 missense_variant ; p.Ser239Gly; MODERATE nonsynonymous_codon ; S239G Average:50.947; most accessible tissue: Zhenshan97 panicle, score: 65.386 probably damaging -2.2 TOLERATED 1.00
vg0517887151 T -> C LOC_Os05g30820.2 missense_variant ; p.Ser239Gly; MODERATE nonsynonymous_codon ; S239G Average:50.947; most accessible tissue: Zhenshan97 panicle, score: 65.386 possibly damaging -1.975 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517887151 NA 1.64E-06 mr1044 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
vg0517887151 NA 1.87E-12 mr1069 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
vg0517887151 NA 7.86E-29 mr1075 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
vg0517887151 NA 1.40E-06 mr1077 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
vg0517887151 NA 2.94E-18 mr1133 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
vg0517887151 NA 3.00E-30 mr1202 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
vg0517887151 NA 6.54E-06 mr1415 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
vg0517887151 NA 6.54E-06 mr1567 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
vg0517887151 NA 9.37E-12 mr1667 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
vg0517887151 NA 9.23E-17 mr1842 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
vg0517887151 NA 5.51E-12 mr1902 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
vg0517887151 NA 5.36E-06 mr1002_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
vg0517887151 NA 6.81E-40 mr1072_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
vg0517887151 NA 4.47E-37 mr1075_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
vg0517887151 NA 3.04E-07 mr1654_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
vg0517887151 NA 1.01E-47 mr1861_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