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Detailed information for vg0120024869:

Variant ID: vg0120024869 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 20024869
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


CTTAGCCATGCTTAGTTCAACTAGTACACAAAGGGGGAATCACATTAATGCATAGACTTTGATTATTGGCATAGCTTTGGATTAATGCCACCGCAATGGT[G/A]
CTAGTTAATTAAAATACACTATATGGTAGGCTGTGGGTGCATGGTTTTGCTAGTCGTGCCCATGACGATTAAGGATCGGTTTGCGGGATGCCCTGGAAGA

Reverse complement sequence

TCTTCCAGGGCATCCCGCAAACCGATCCTTAATCGTCATGGGCACGACTAGCAAAACCATGCACCCACAGCCTACCATATAGTGTATTTTAATTAACTAG[C/T]
ACCATTGCGGTGGCATTAATCCAAAGCTATGCCAATAATCAAAGTCTATGCATTAATGTGATTCCCCCTTTGTGTACTAGTTGAACTAAGCATGGCTAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.70% 37.20% 0.02% 0.08% NA
All Indica  2759 36.60% 63.20% 0.04% 0.14% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 15.60% 84.40% 0.00% 0.00% NA
Indica II  465 62.60% 37.00% 0.00% 0.43% NA
Indica III  913 30.80% 69.20% 0.00% 0.00% NA
Indica Intermediate  786 44.00% 55.60% 0.13% 0.25% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0120024869 G -> A LOC_Os01g36200.1 upstream_gene_variant ; 1429.0bp to feature; MODIFIER silent_mutation Average:46.258; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0120024869 G -> A LOC_Os01g36200-LOC_Os01g36220 intergenic_region ; MODIFIER silent_mutation Average:46.258; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0120024869 G -> DEL N N silent_mutation Average:46.258; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0120024869 NA 7.04E-10 mr1195 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
vg0120024869 NA 1.20E-12 mr1362 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
vg0120024869 NA 1.10E-09 mr1565 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
vg0120024869 NA 7.66E-08 mr1836 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
vg0120024869 NA 7.01E-06 mr1053_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
vg0120024869 NA 1.12E-12 mr1147_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
vg0120024869 NA 4.92E-06 mr1402_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
vg0120024869 NA 4.50E-09 mr1565_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
vg0120024869 NA 2.40E-09 mr1624_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
vg0120024869 NA 5.46E-07 mr1624_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
vg0120024869 4.08E-06 NA mr1739_2 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
vg0120024869 NA 3.59E-09 mr1739_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
vg0120024869 NA 1.94E-06 mr1901_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
vg0120024869 NA 1.28E-06 mr1959_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