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Detailed information for vg0519106763:

Variant ID: vg0519106763 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19106763
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTATTTATATATTTATATAATTTTACACGGTAGTTACAACACACTTACACATCAGTTACGTATGTAAACTCGACTTACACATCACTTACATATGTAAT[T/C]
AGTATGTAATTTTGGGATTTACATATGTAATTTTAGGACTTACATATGTAATTTTGGGAGTTACATTGTAAATATAATAAAATTACATATGTAATTTTGG

Reverse complement sequence

CCAAAATTACATATGTAATTTTATTATATTTACAATGTAACTCCCAAAATTACATATGTAAGTCCTAAAATTACATATGTAAATCCCAAAATTACATACT[A/G]
ATTACATATGTAAGTGATGTGTAAGTCGAGTTTACATACGTAACTGATGTGTAAGTGTGTTGTAACTACCGTGTAAAATTATATAAATATATAAATAACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.60% 34.90% 0.51% 0.00% NA
All Indica  2759 55.80% 43.40% 0.80% 0.00% NA
All Japonica  1512 87.00% 12.90% 0.07% 0.00% NA
Aus  269 14.10% 85.90% 0.00% 0.00% NA
Indica I  595 28.10% 71.30% 0.67% 0.00% NA
Indica II  465 60.90% 38.10% 1.08% 0.00% NA
Indica III  913 63.20% 36.10% 0.66% 0.00% NA
Indica Intermediate  786 65.30% 33.80% 0.89% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 69.60% 30.20% 0.20% 0.00% NA
Japonica Intermediate  241 86.30% 13.70% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg0519106763 T -> C LOC_Os05g32620.1 downstream_gene_variant ; 1804.0bp to feature; MODIFIER silent_mutation Average:35.085; most accessible tissue: Callus, score: 66.538 N N N N
vg0519106763 T -> C LOC_Os05g32630.1 downstream_gene_variant ; 1799.0bp to feature; MODIFIER silent_mutation Average:35.085; most accessible tissue: Callus, score: 66.538 N N N N
vg0519106763 T -> C LOC_Os05g32620-LOC_Os05g32630 intergenic_region ; MODIFIER silent_mutation Average:35.085; most accessible tissue: Callus, score: 66.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519106763 NA 4.51E-06 mr1044 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
vg0519106763 NA 8.43E-06 mr1199 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
vg0519106763 NA 7.46E-08 mr1676 Jap_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
vg0519106763 NA 3.55E-07 mr1830 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
vg0519106763 NA 2.38E-07 mr1951 Jap_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
vg0519106763 NA 9.20E-08 mr1131_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
vg0519106763 NA 6.31E-09 mr1199_2 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
vg0519106763 NA 3.89E-06 mr1325_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
vg0519106763 NA 2.07E-06 mr1333_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
vg0519106763 NA 1.61E-08 mr1482_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
vg0519106763 NA 3.07E-06 mr1482_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
vg0519106763 NA 8.92E-09 mr1676_2 Jap_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
vg0519106763 NA 5.49E-06 mr1763_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
vg0519106763 NA 1.26E-14 mr1769_2 Jap_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
vg0519106763 NA 4.54E-07 mr1830_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
vg0519106763 NA 1.17E-08 mr1846_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