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Detailed information for vg1116906179:

Variant ID: vg1116906179 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16906179
Reference Allele: AAlternative Allele: G,T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


AAGATCGGTAAAGATCGAAAAGAGCAAACGTGGCTCTGATACCACTGGTAGGATCGAATCACAAGAACTAAGCCAACCAGAGGGGGGGTGAATGGTTGGT[A/G,T]
TACCCAAAAACCAAAAACTTTTAGCGGAAATAAAAGTTACCCTCGAAATCGATGGATCGCGGTCTGACTAAAGTAGTTGCACCAGTCTAACCGCCTGGAA

Reverse complement sequence

TTCCAGGCGGTTAGACTGGTGCAACTACTTTAGTCAGACCGCGATCCATCGATTTCGAGGGTAACTTTTATTTCCGCTAAAAGTTTTTGGTTTTTGGGTA[T/C,A]
ACCAACCATTCACCCCCCCTCTGGTTGGCTTAGTTCTTGTGATTCGATCCTACCAGTGGTATCAGAGCCACGTTTGCTCTTTTCGATCTTTACCGATCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.30% 16.90% 3.68% 0.04% G: 1.04%
All Indica  2759 66.20% 26.10% 5.91% 0.07% G: 1.67%
All Japonica  1512 96.00% 3.80% 0.13% 0.00% G: 0.07%
Aus  269 95.50% 3.70% 0.37% 0.00% G: 0.37%
Indica I  595 79.70% 9.40% 10.59% 0.00% G: 0.34%
Indica II  465 53.80% 39.80% 4.95% 0.22% G: 1.29%
Indica III  913 66.50% 26.70% 4.05% 0.11% G: 2.63%
Indica Intermediate  786 63.10% 30.00% 5.09% 0.00% G: 1.78%
Temperate Japonica  767 97.90% 2.00% 0.13% 0.00% NA
Tropical Japonica  504 95.80% 4.00% 0.00% 0.00% G: 0.20%
Japonica Intermediate  241 90.50% 9.10% 0.41% 0.00% NA
VI/Aromatic  96 96.90% 0.00% 2.08% 0.00% G: 1.04%
Intermediate  90 78.90% 14.40% 6.67% 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
vg1116906179 A -> T LOC_Os11g29160.1 upstream_gene_variant ; 112.0bp to feature; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> T LOC_Os11g29170.1 upstream_gene_variant ; 2575.0bp to feature; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> T LOC_Os11g29160-LOC_Os11g29170 intergenic_region ; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> DEL N N silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> G LOC_Os11g29160.1 upstream_gene_variant ; 112.0bp to feature; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> G LOC_Os11g29170.1 upstream_gene_variant ; 2575.0bp to feature; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg1116906179 A -> G LOC_Os11g29160-LOC_Os11g29170 intergenic_region ; MODIFIER silent_mutation Average:20.44; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116906179 1.15E-07 NA mr1144 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
vg1116906179 2.15E-07 7.31E-07 mr1144 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