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Detailed information for vg1115402655:

Variant ID: vg1115402655 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15402655
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGAGATGTGAGTCTCAGATCTCACAAAAACTGGCTCCCTAAACATATCACAATTCTTTGATCTATATTTTGCAGTAGTGTAGTAAACATAAGATAAAA[C/T]
ACATAGGTGATGAAACAAACAAGCAGAGAAGGGTCTTGTAGCTTGCTTCCTGGCAGAAGGAGCCAAGTGATCACCAAGCATATTACTATGGCAGTCCCTG

Reverse complement sequence

CAGGGACTGCCATAGTAATATGCTTGGTGATCACTTGGCTCCTTCTGCCAGGAAGCAAGCTACAAGACCCTTCTCTGCTTGTTTGTTTCATCACCTATGT[G/A]
TTTTATCTTATGTTTACTACACTACTGCAAAATATAGATCAAAGAATTGTGATATGTTTAGGGAGCCAGTTTTTGTGAGATCTGAGACTCACATCTCTGA

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 94.10% 5.90% 0.02% 0.00% NA
All Indica  2759 90.90% 9.10% 0.04% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 77.00% 22.90% 0.17% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 89.80% 10.20% 0.00% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1115402655 C -> T LOC_Os11g26830.1 downstream_gene_variant ; 1785.0bp to feature; MODIFIER silent_mutation Average:40.264; most accessible tissue: Callus, score: 56.956 N N N N
vg1115402655 C -> T LOC_Os11g26810-LOC_Os11g26830 intergenic_region ; MODIFIER silent_mutation Average:40.264; most accessible tissue: Callus, score: 56.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115402655 2.58E-06 NA mr1097_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
vg1115402655 7.75E-06 7.95E-07 mr1097_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
vg1115402655 3.40E-06 NA mr1154_2 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
vg1115402655 1.04E-06 3.76E-07 mr1154_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