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Detailed information for vg1125096005:

Variant ID: vg1125096005 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25096005
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTCAAGTAGTATATATATACTTCTTTCGTCCCAAAATAGACTAATCTCATGCGAAATGTGACACATCGTAGTACTACGAATCTAGAACTGAAACGGGG[T/G]
TTGGAACTATTCCGGCTCACATAATATAATGGAGCAGCCGCTCATGCTTACATGCTCACTAGCAATGTATACTCCTACATTGTAGCATGTAATTAAGTAC

Reverse complement sequence

GTACTTAATTACATGCTACAATGTAGGAGTATACATTGCTAGTGAGCATGTAAGCATGAGCGGCTGCTCCATTATATTATGTGAGCCGGAATAGTTCCAA[A/C]
CCCCGTTTCAGTTCTAGATTCGTAGTACTACGATGTGTCACATTTCGCATGAGATTAGTCTATTTTGGGACGAAAGAAGTATATATATACTACTTGAAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 1.00% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.10% 2.80% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 94.90% 5.00% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1125096005 T -> G LOC_Os11g41770.1 downstream_gene_variant ; 4782.0bp to feature; MODIFIER silent_mutation Average:41.03; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N
vg1125096005 T -> G LOC_Os11g41760-LOC_Os11g41770 intergenic_region ; MODIFIER silent_mutation Average:41.03; 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
vg1125096005 NA 5.26E-06 mr1100_2 Jap_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
vg1125096005 NA 3.26E-06 mr1402_2 Jap_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
vg1125096005 NA 2.35E-06 mr1613_2 Jap_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
vg1125096005 1.61E-08 1.89E-10 mr1795_2 Jap_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
vg1125096005 NA 6.96E-06 mr1913_2 Jap_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
vg1125096005 NA 6.99E-07 mr1962_2 Jap_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