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Detailed information for vg1109787121:

Variant ID: vg1109787121 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9787121
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.85, T: 0.16, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GGCAATAATAACTAGAATAGGGAGGACTCCAGAGGAGTATATGTGGTTTTCACATTTTTTGTTCTCTTTTTCTTCTCTTTCTATCATGAAGATTTTTTTT[A/T]
AAAAAATCAAGCTTAATTTTGGATTATGCTATTCCTTTCAATCTGGTCAAAGTTAGCTATGATTCTTCCTCCCTTCTCTATATATCGAACCGTTCTTCCA

Reverse complement sequence

TGGAAGAACGGTTCGATATATAGAGAAGGGAGGAAGAATCATAGCTAACTTTGACCAGATTGAAAGGAATAGCATAATCCAAAATTAAGCTTGATTTTTT[T/A]
AAAAAAAATCTTCATGATAGAAAGAGAAGAAAAAGAGAACAAAAAATGTGAAAACCACATATACTCCTCTGGAGTCCTCCCTATTCTAGTTATTATTGCC

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 56.70% 43.10% 0.21% 0.00% NA
All Indica  2759 35.60% 64.00% 0.36% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 19.30% 80.70% 0.00% 0.00% NA
Indica I  595 24.00% 75.30% 0.67% 0.00% NA
Indica II  465 65.40% 34.20% 0.43% 0.00% NA
Indica III  913 18.20% 81.50% 0.33% 0.00% NA
Indica Intermediate  786 47.10% 52.80% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.80% 2.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg1109787121 A -> T LOC_Os11g17570.1 downstream_gene_variant ; 1620.0bp to feature; MODIFIER silent_mutation Average:45.845; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg1109787121 A -> T LOC_Os11g17580.1 downstream_gene_variant ; 886.0bp to feature; MODIFIER silent_mutation Average:45.845; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg1109787121 A -> T LOC_Os11g17570-LOC_Os11g17580 intergenic_region ; MODIFIER silent_mutation Average:45.845; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109787121 NA 4.78E-11 mr1097 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
vg1109787121 NA 1.57E-08 mr1092_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
vg1109787121 NA 3.89E-15 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
vg1109787121 6.47E-06 9.88E-12 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
vg1109787121 NA 2.48E-06 mr1102_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
vg1109787121 NA 1.23E-07 mr1152_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
vg1109787121 NA 2.66E-13 mr1154_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