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Detailed information for vg0207836464:

Variant ID: vg0207836464 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7836464
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGTAGAAAATAATTTTATCAATAAACTACAACATTAACAAATTATGTACGCATGACAGGCGGCTGCGTTAGATAGGATGGGTTGGGAACCCATCCCCTT[C/T]
CCACGGAAAATGGAGTAGTCCATTAGCACATGATTAATTAAGTATTAACTATTTTTTAAAAAAAATAGATTAATTTGATTTTTTTAACTAACTTTTTTAT

Reverse complement sequence

ATAAAAAAGTTAGTTAAAAAAATCAAATTAATCTATTTTTTTTAAAAAATAGTTAATACTTAATTAATCATGTGCTAATGGACTACTCCATTTTCCGTGG[G/A]
AAGGGGATGGGTTCCCAACCCATCCTATCTAACGCAGCCGCCTGTCATGCGTACATAATTTGTTAATGTTGTAGTTTATTGATAAAATTATTTTCTACGG

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 97.70% 1.40% 0.85% 0.00% NA
All Indica  2759 96.10% 2.40% 1.45% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 89.10% 6.10% 4.87% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 95.20% 3.70% 1.15% 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  241 100.00% 0.00% 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
vg0207836464 C -> T LOC_Os02g14280.1 upstream_gene_variant ; 3141.0bp to feature; MODIFIER silent_mutation Average:46.621; most accessible tissue: Callus, score: 79.494 N N N N
vg0207836464 C -> T LOC_Os02g14260-LOC_Os02g14280 intergenic_region ; MODIFIER silent_mutation Average:46.621; most accessible tissue: Callus, score: 79.494 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207836464 4.57E-06 1.72E-06 mr1520 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
vg0207836464 NA 6.25E-06 mr1320_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
vg0207836464 NA 6.67E-07 mr1696_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