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Detailed information for vg1125960837:

Variant ID: vg1125960837 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25960837
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.83, G: 0.17, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GAGGAGATCACAATTATTGAAGGAATGTAAGTGAGGGCCTTGAAATAAAGCAGAACACATATATAATGCATTTACTAGTTGATATCATGCGTTTTGCTAC[A/G]
GGATGTGGATTAATGCACGTTATATGTATATCGATCCTTGTGTGCATTTTACAAACATAAATGCAGAATGAACTAAGATAGTCCTTTATAAGTTAATGAG

Reverse complement sequence

CTCATTAACTTATAAAGGACTATCTTAGTTCATTCTGCATTTATGTTTGTAAAATGCACACAAGGATCGATATACATATAACGTGCATTAATCCACATCC[T/C]
GTAGCAAAACGCATGATATCAACTAGTAAATGCATTATATATGTGTTCTGCTTTATTTCAAGGCCCTCACTTACATTCCTTCAATAATTGTGATCTCCTC

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 62.80% 34.20% 0.06% 2.94% NA
All Indica  2759 45.90% 49.10% 0.07% 4.93% NA
All Japonica  1512 93.20% 6.80% 0.00% 0.00% NA
Aus  269 52.80% 46.80% 0.37% 0.00% NA
Indica I  595 59.00% 40.70% 0.34% 0.00% NA
Indica II  465 39.10% 60.60% 0.00% 0.22% NA
Indica III  913 32.00% 54.90% 0.00% 13.14% NA
Indica Intermediate  786 56.20% 41.90% 0.00% 1.91% NA
Temperate Japonica  767 96.90% 3.10% 0.00% 0.00% NA
Tropical Japonica  504 87.50% 12.50% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 61.10% 35.60% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125960837 A -> DEL N N silent_mutation Average:18.829; most accessible tissue: Minghui63 root, score: 35.002 N N N N
vg1125960837 A -> G LOC_Os11g43040-LOC_Os11g43060 intergenic_region ; MODIFIER silent_mutation Average:18.829; most accessible tissue: Minghui63 root, score: 35.002 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125960837 1.74E-09 9.48E-14 mr1191 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
vg1125960837 1.54E-11 2.34E-11 mr1191 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
vg1125960837 7.72E-14 1.68E-14 mr1644 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
vg1125960837 2.62E-15 2.31E-12 mr1644 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
vg1125960837 1.62E-14 4.39E-20 mr1191_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
vg1125960837 6.85E-16 4.08E-14 mr1191_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
vg1125960837 NA 2.40E-06 mr1925_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