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Detailed information for vg0118023767:

Variant ID: vg0118023767 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18023767
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AAAACTAGAGCTTCACATAGACAGATACCTAATTTGTTGTCACTGGTAAGCATGTTGTCGTTAGAGGATTTTACAGTTTTCTGAAGTTTGTAATTAATTC[G/A]
GTTCCTTTTTAATGGGTTTCTCATTGAAATCGAGAGGGAAAGAACCAAACAAGCAAACAATTGAAATTAAAAGTAAGCTTGTTTTCTGCTTCACTTCATC

Reverse complement sequence

GATGAAGTGAAGCAGAAAACAAGCTTACTTTTAATTTCAATTGTTTGCTTGTTTGGTTCTTTCCCTCTCGATTTCAATGAGAAACCCATTAAAAAGGAAC[C/T]
GAATTAATTACAAACTTCAGAAAACTGTAAAATCCTCTAACGACAACATGCTTACCAGTGACAACAAATTAGGTATCTGTCTATGTGAAGCTCTAGTTTT

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 52.90% 34.50% 0.36% 12.21% NA
All Indica  2759 76.70% 2.20% 0.58% 20.48% NA
All Japonica  1512 9.50% 90.30% 0.00% 0.20% NA
Aus  269 75.10% 24.90% 0.00% 0.00% NA
Indica I  595 52.60% 0.70% 0.84% 45.88% NA
Indica II  465 68.00% 4.50% 0.86% 26.67% NA
Indica III  913 97.60% 0.40% 0.00% 1.97% NA
Indica Intermediate  786 76.00% 4.10% 0.89% 19.08% NA
Temperate Japonica  767 5.30% 94.70% 0.00% 0.00% NA
Tropical Japonica  504 6.50% 93.10% 0.00% 0.40% NA
Japonica Intermediate  241 29.00% 70.50% 0.00% 0.41% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 36.70% 52.20% 1.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0118023767 G -> A LOC_Os01g32849.1 downstream_gene_variant ; 2737.0bp to feature; MODIFIER silent_mutation Average:34.465; most accessible tissue: Callus, score: 68.73 N N N N
vg0118023767 G -> A LOC_Os01g32840.1 intron_variant ; MODIFIER silent_mutation Average:34.465; most accessible tissue: Callus, score: 68.73 N N N N
vg0118023767 G -> DEL N N silent_mutation Average:34.465; most accessible tissue: Callus, score: 68.73 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118023767 NA 1.59E-15 mr1228 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
vg0118023767 NA 3.11E-19 mr1242 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
vg0118023767 NA 3.97E-28 mr1298 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
vg0118023767 NA 2.19E-51 mr1519 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
vg0118023767 NA 1.31E-20 mr1698 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
vg0118023767 3.15E-06 2.84E-07 mr1719 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
vg0118023767 NA 2.38E-17 mr1825 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
vg0118023767 5.06E-06 1.87E-54 mr1519_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
vg0118023767 NA 1.93E-06 mr1519_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
vg0118023767 NA 6.32E-22 mr1698_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
vg0118023767 NA 6.92E-07 mr1727_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