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Detailed information for vg1214119394:

Variant ID: vg1214119394 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14119394
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATATAAAGATATCATAAATTTAGACTTGGATATATAATATACAACACGTTGATTGGATGCAGTTTATTCTAATATAACAGTTGCATGGTCTGATGTTGC[C/A]
TGAAAATTTACATTACTAAACATACCATATAAATTCTAGAAAATTTATTTAATTTTTCAAAATTATTATCCAAATAAAATTCAAATGCATAAGTAAATGT

Reverse complement sequence

ACATTTACTTATGCATTTGAATTTTATTTGGATAATAATTTTGAAAAATTAAATAAATTTTCTAGAATTTATATGGTATGTTTAGTAATGTAAATTTTCA[G/T]
GCAACATCAGACCATGCAACTGTTATATTAGAATAAACTGCATCCAATCAACGTGTTGTATATTATATATCCAAGTCTAAATTTATGATATCTTTATATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.40% 1.30% 0.30% 0.00% NA
All Indica  2759 97.30% 2.20% 0.51% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.90% 6.10% 2.02% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.60% 1.40% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.30% 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  241 100.00% 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
vg1214119394 C -> A LOC_Os12g24650.1 downstream_gene_variant ; 4886.0bp to feature; MODIFIER silent_mutation Average:25.922; most accessible tissue: Zhenshan97 young leaf, score: 46.636 N N N N
vg1214119394 C -> A LOC_Os12g24659.1 downstream_gene_variant ; 3495.0bp to feature; MODIFIER silent_mutation Average:25.922; most accessible tissue: Zhenshan97 young leaf, score: 46.636 N N N N
vg1214119394 C -> A LOC_Os12g24650-LOC_Os12g24659 intergenic_region ; MODIFIER silent_mutation Average:25.922; most accessible tissue: Zhenshan97 young leaf, score: 46.636 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214119394 1.23E-06 7.27E-09 mr1088 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
vg1214119394 NA 2.79E-06 mr1104 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
vg1214119394 3.04E-06 9.69E-09 mr1246 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
vg1214119394 1.09E-06 7.74E-06 mr1437 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
vg1214119394 NA 7.92E-06 mr1220_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
vg1214119394 NA 2.15E-07 mr1517_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