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Detailed information for vg0912154976:

Variant ID: vg0912154976 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 12154976
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


CACACCATTTACACATGTAAAAACTATATAATTTTGAGACTTACATATGTAATTTTGAAACTTATATTATAAATACACTAAATTTACATATGTAATTTAG[A/G]
GACTTACAATATAAATACGTGTTGCCTATTTTTTAAGTAAAAAATACGGCGCTATAAATATAACTACACCGGACCCTTGAGAATTTTATGCGTACAGGTC

Reverse complement sequence

GACCTGTACGCATAAAATTCTCAAGGGTCCGGTGTAGTTATATTTATAGCGCCGTATTTTTTACTTAAAAAATAGGCAACACGTATTTATATTGTAAGTC[T/C]
CTAAATTACATATGTAAATTTAGTGTATTTATAATATAAGTTTCAAAATTACATATGTAAGTCTCAAAATTATATAGTTTTTACATGTGTAAATGGTGTG

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 60.60% 39.00% 0.21% 0.13% NA
All Indica  2759 43.30% 56.30% 0.25% 0.22% NA
All Japonica  1512 97.40% 2.50% 0.07% 0.00% NA
Aus  269 22.30% 77.70% 0.00% 0.00% NA
Indica I  595 57.80% 42.20% 0.00% 0.00% NA
Indica II  465 71.40% 28.20% 0.43% 0.00% NA
Indica III  913 24.00% 75.70% 0.11% 0.22% NA
Indica Intermediate  786 38.00% 60.90% 0.51% 0.51% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 93.80% 5.80% 0.41% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 75.60% 22.20% 2.22% 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
vg0912154976 A -> G LOC_Os09g20270.1 upstream_gene_variant ; 2229.0bp to feature; MODIFIER silent_mutation Average:38.079; most accessible tissue: Callus, score: 77.928 N N N N
vg0912154976 A -> G LOC_Os09g20260-LOC_Os09g20270 intergenic_region ; MODIFIER silent_mutation Average:38.079; most accessible tissue: Callus, score: 77.928 N N N N
vg0912154976 A -> DEL N N silent_mutation Average:38.079; most accessible tissue: Callus, score: 77.928 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0912154976 NA 2.86E-06 mr1057 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
vg0912154976 NA 9.60E-06 mr1140 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
vg0912154976 NA 2.03E-07 mr1613 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
vg0912154976 3.83E-06 NA mr1024_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
vg0912154976 NA 3.86E-10 mr1057_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
vg0912154976 NA 3.94E-06 mr1071_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
vg0912154976 NA 4.47E-07 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
vg0912154976 NA 9.34E-08 mr1126_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
vg0912154976 NA 6.88E-06 mr1127_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
vg0912154976 NA 2.14E-06 mr1203_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
vg0912154976 NA 2.73E-08 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
vg0912154976 NA 2.36E-06 mr1762_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
vg0912154976 NA 1.31E-07 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