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Detailed information for vg1115482640:

Variant ID: vg1115482640 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15482640
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TAATTAGGTGAGTACCTATTATTGTAAAACCCTTAGTATTGTAGAACTTTAATGTATGCAATTAAGAACCAGTTATATTGTATGTATCAATATTTACTGA[T/A]
CCAGGGATTGATACATTAATCATAGTCGGATCCAAGTAATTAGTTCTGGGACCCGACGGACATGTAAACATTGTCTTGCTTTGATCATCGGCATAGATGG

Reverse complement sequence

CCATCTATGCCGATGATCAAAGCAAGACAATGTTTACATGTCCGTCGGGTCCCAGAACTAATTACTTGGATCCGACTATGATTAATGTATCAATCCCTGG[A/T]
TCAGTAAATATTGATACATACAATATAACTGGTTCTTAATTGCATACATTAAAGTTCTACAATACTAAGGGTTTTACAATAATAGGTACTCACCTAATTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 3.60% 0.06% 1.35% NA
All Indica  2759 91.70% 5.90% 0.11% 2.32% 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 82.00% 17.80% 0.17% 0.00% NA
Indica II  465 99.10% 0.20% 0.00% 0.65% NA
Indica III  913 93.80% 1.60% 0.00% 4.60% NA
Indica Intermediate  786 92.20% 5.10% 0.25% 2.42% NA
Temperate Japonica  767 99.90% 0.10% 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 93.30% 6.70% 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
vg1115482640 T -> A LOC_Os11g26930.1 upstream_gene_variant ; 3127.0bp to feature; MODIFIER silent_mutation Average:32.086; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N
vg1115482640 T -> A LOC_Os11g26920-LOC_Os11g26930 intergenic_region ; MODIFIER silent_mutation Average:32.086; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N
vg1115482640 T -> DEL N N silent_mutation Average:32.086; most accessible tissue: Zhenshan97 young leaf, score: 51.997 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115482640 8.76E-07 5.60E-06 mr1154 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
vg1115482640 5.34E-11 3.36E-11 mr1097_2 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
vg1115482640 2.10E-09 6.79E-09 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
vg1115482640 NA 9.44E-06 mr1223_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