Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0506765429:

Variant ID: vg0506765429 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6765429
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTAATTTTTGATTTCTCATCTTTTTCAAAGTAAAATAGATAAAACTTATTTGTGAGATTATTCAATAGTTTACATTGAAAGAATTTAGCAATAAAGA[C/T]
TAGTTTTAAACTTTCAATGATATTATTAAAGAGGTAAAATTTAAGTTTTTTTTAAATGACTAGTTTATGTATTGATTGTTATTAACGGTAACTATTTGAC

Reverse complement sequence

GTCAAATAGTTACCGTTAATAACAATCAATACATAAACTAGTCATTTAAAAAAAACTTAAATTTTACCTCTTTAATAATATCATTGAAAGTTTAAAACTA[G/A]
TCTTTATTGCTAAATTCTTTCAATGTAAACTATTGAATAATCTCACAAATAAGTTTTATCTATTTTACTTTGAAAAAGATGAGAAATCAAAAATTAATTT

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 98.00% 2.00% 0.04% 0.00% NA
All Indica  2759 96.60% 3.30% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.30% 0.25% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 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
vg0506765429 C -> T LOC_Os05g11860.1 upstream_gene_variant ; 3928.0bp to feature; MODIFIER silent_mutation Average:31.901; most accessible tissue: Callus, score: 74.943 N N N N
vg0506765429 C -> T LOC_Os05g11870.1 upstream_gene_variant ; 1065.0bp to feature; MODIFIER silent_mutation Average:31.901; most accessible tissue: Callus, score: 74.943 N N N N
vg0506765429 C -> T LOC_Os05g11860-LOC_Os05g11870 intergenic_region ; MODIFIER silent_mutation Average:31.901; most accessible tissue: Callus, score: 74.943 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506765429 1.09E-07 NA mr1004 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
vg0506765429 4.46E-06 NA mr1005 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