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Detailed information for vg0224012738:

Variant ID: vg0224012738 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24012738
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: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTATTAATACCGTATAGTGTTCTTTTAATATTTTTATTTTTTATTTTTGAATTTAAGTTGTTTCAAAATTGTATTCCTACTTGAACTCTCTTTTAG[T/C]
TTTTCTAATTTTGGATATTGTTTTATTTTTTATTCTGAATTTTAACTAATCTCATATCGGGTTCTTATATATCTCATATCGGGTTCTTATATGTATTCTT

Reverse complement sequence

AAGAATACATATAAGAACCCGATATGAGATATATAAGAACCCGATATGAGATTAGTTAAAATTCAGAATAAAAAATAAAACAATATCCAAAATTAGAAAA[A/G]
CTAAAAGAGAGTTCAAGTAGGAATACAATTTTGAAACAACTTAAATTCAAAAATAAAAAATAAAAATATTAAAAGAACACTATACGGTATTAATAAAAAT

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 78.80% 11.80% 8.68% 0.76% NA
All Indica  2759 74.40% 10.80% 13.63% 1.16% NA
All Japonica  1512 97.20% 0.80% 1.79% 0.20% NA
Aus  269 33.50% 65.80% 0.37% 0.37% NA
Indica I  595 86.70% 0.50% 11.76% 1.01% NA
Indica II  465 58.50% 20.90% 18.71% 1.94% NA
Indica III  913 78.80% 10.30% 10.62% 0.33% NA
Indica Intermediate  786 69.30% 13.40% 15.52% 1.78% NA
Temperate Japonica  767 99.00% 0.00% 0.91% 0.13% NA
Tropical Japonica  504 94.00% 2.00% 3.57% 0.40% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 0.00% NA
VI/Aromatic  96 39.60% 58.30% 2.08% 0.00% NA
Intermediate  90 82.20% 13.30% 4.44% 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
vg0224012738 T -> DEL N N silent_mutation Average:17.871; most accessible tissue: Callus, score: 41.96 N N N N
vg0224012738 T -> C LOC_Os02g39750-LOC_Os02g39764 intergenic_region ; MODIFIER silent_mutation Average:17.871; most accessible tissue: Callus, score: 41.96 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224012738 4.37E-06 NA mr1069 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
vg0224012738 NA 1.81E-06 mr1069 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
vg0224012738 NA 6.88E-06 mr1103 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
vg0224012738 NA 1.99E-06 mr1149 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
vg0224012738 NA 1.75E-06 mr1202 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
vg0224012738 NA 1.33E-06 mr1503 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
vg0224012738 NA 3.26E-09 mr1072_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
vg0224012738 NA 3.29E-09 mr1075_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
vg0224012738 NA 9.38E-08 mr1149_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
vg0224012738 NA 8.21E-06 mr1402_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
vg0224012738 NA 3.61E-08 mr1441_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
vg0224012738 NA 8.16E-06 mr1795_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