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Detailed information for vg1113530105:

Variant ID: vg1113530105 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13530105
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTTACTCATTAATTGCTCAATAAAATTAGCTTTATGCAAATGTTGAACCTAGAGACCCACTATAGGCTAGAAAGCTTGCATACTTCTCTCTCCCTTAT[A/G]
TATATATAATTTTGGGTAAGACTTGCGAGTACAATCTTGTACTTAAACCGGTGTCTGCAATTTCAGGAGAGGATTCCGGTTATGAGTTATGTTTCTTGTG

Reverse complement sequence

CACAAGAAACATAACTCATAACCGGAATCCTCTCCTGAAATTGCAGACACCGGTTTAAGTACAAGATTGTACTCGCAAGTCTTACCCAAAATTATATATA[T/C]
ATAAGGGAGAGAGAAGTATGCAAGCTTTCTAGCCTATAGTGGGTCTCTAGGTTCAACATTTGCATAAAGCTAATTTTATTGAGCAATTAATGAGTAAAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 0.30% 0.89% 1.78% NA
All Indica  2759 95.20% 0.50% 1.38% 2.97% NA
All Japonica  1512 99.70% 0.10% 0.13% 0.13% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.10% 0.50% 0.84% 3.53% NA
Indica II  465 96.80% 0.60% 1.72% 0.86% NA
Indica III  913 94.40% 0.40% 0.77% 4.38% NA
Indica Intermediate  786 95.20% 0.40% 2.29% 2.16% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.20% 0.40% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1113530105 A -> DEL N N silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23880.1 downstream_gene_variant ; 3848.0bp to feature; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23890.1 downstream_gene_variant ; 2298.0bp to feature; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23880.4 downstream_gene_variant ; 3840.0bp to feature; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23880.2 downstream_gene_variant ; 3848.0bp to feature; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23880.3 downstream_gene_variant ; 3848.0bp to feature; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N
vg1113530105 A -> G LOC_Os11g23880-LOC_Os11g23890 intergenic_region ; MODIFIER silent_mutation Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1113530105 4.43E-06 NA mr1619 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