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Detailed information for vg1111385027:

Variant ID: vg1111385027 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 11385027
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AAGACACATGGTGAATGGGGAGAACTCAAAAGCATGTTTTGTCTTGCTTTCTTCCTGTTAACCCGTGATGTCTTCCTATGGATGGAAATTCTCGGCTTTT[A/G]
GCAGAGTGAGAAGAAGTCTGCCTCGTATGTTGATTTTTTCACCGGAGGCTAGTCGCACTGCAGAAGGTAGGGATTGTATCGTAGAGAACACCTCCCATCG

Reverse complement sequence

CGATGGGAGGTGTTCTCTACGATACAATCCCTACCTTCTGCAGTGCGACTAGCCTCCGGTGAAAAAATCAACATACGAGGCAGACTTCTTCTCACTCTGC[T/C]
AAAAGCCGAGAATTTCCATCCATAGGAAGACATCACGGGTTAACAGGAAGAAAGCAAGACAAAACATGCTTTTGAGTTCTCCCCATTCACCATGTGTCTT

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 93.10% 5.40% 1.46% 0.00% NA
All Indica  2759 88.70% 9.00% 2.32% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 0.20% 5.04% 0.00% NA
Indica II  465 81.10% 15.30% 3.66% 0.00% NA
Indica III  913 89.70% 10.00% 0.33% 0.00% NA
Indica Intermediate  786 87.30% 10.90% 1.78% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 3.33% 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
vg1111385027 A -> G LOC_Os11g19760.1 downstream_gene_variant ; 1178.0bp to feature; MODIFIER silent_mutation Average:58.62; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N
vg1111385027 A -> G LOC_Os11g19764.1 downstream_gene_variant ; 1167.0bp to feature; MODIFIER silent_mutation Average:58.62; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N
vg1111385027 A -> G LOC_Os11g19764.2 downstream_gene_variant ; 3257.0bp to feature; MODIFIER silent_mutation Average:58.62; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N
vg1111385027 A -> G LOC_Os11g19764.3 downstream_gene_variant ; 3257.0bp to feature; MODIFIER silent_mutation Average:58.62; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N
vg1111385027 A -> G LOC_Os11g19760-LOC_Os11g19764 intergenic_region ; MODIFIER silent_mutation Average:58.62; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1111385027 9.20E-06 NA mr1113_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
vg1111385027 8.73E-06 NA mr1117_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
vg1111385027 9.39E-06 NA mr1119_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
vg1111385027 1.98E-06 NA mr1120_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
vg1111385027 5.77E-07 NA mr1247_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