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Detailed information for vg1209679986:

Variant ID: vg1209679986 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 9679986
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


CAATACGTGTTAGCTGAGCTGTTATGAGAAATAATGTCTCCTCTGTCACGATTTCGTTTCCTTTCGTGATTTTTTCTCTCTAACGTGTTTTTTAACTCCT[T/C]
GGCAAAATAAACGCAAGCTAATCTTTCAGATTTTTTTCCAAAGTGGTCATAAAATCGATGACGTTCTTAAAGGCTATGATAAGATTTTTAACACGGAATG

Reverse complement sequence

CATTCCGTGTTAAAAATCTTATCATAGCCTTTAAGAACGTCATCGATTTTATGACCACTTTGGAAAAAAATCTGAAAGATTAGCTTGCGTTTATTTTGCC[A/G]
AGGAGTTAAAAAACACGTTAGAGAGAAAAAATCACGAAAGGAAACGAAATCGTGACAGAGGAGACATTATTTCTCATAACAGCTCAGCTAACACGTATTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.80% 36.40% 0.38% 25.37% NA
All Indica  2759 41.00% 19.40% 0.51% 39.07% NA
All Japonica  1512 22.30% 74.40% 0.00% 3.31% NA
Aus  269 80.70% 3.00% 0.37% 15.99% NA
Indica I  595 55.10% 28.40% 0.84% 15.63% NA
Indica II  465 39.10% 30.50% 0.22% 30.11% NA
Indica III  913 30.10% 5.80% 0.77% 63.31% NA
Indica Intermediate  786 44.00% 21.90% 0.13% 33.97% NA
Temperate Japonica  767 9.40% 85.00% 0.00% 5.61% NA
Tropical Japonica  504 31.90% 66.90% 0.00% 1.19% NA
Japonica Intermediate  241 43.20% 56.40% 0.00% 0.41% NA
VI/Aromatic  96 65.60% 9.40% 2.08% 22.92% NA
Intermediate  90 44.40% 47.80% 1.11% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1209679986 T -> C LOC_Os12g16870.1 upstream_gene_variant ; 4371.0bp to feature; MODIFIER silent_mutation Average:37.649; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N
vg1209679986 T -> C LOC_Os12g16870-LOC_Os12g16880 intergenic_region ; MODIFIER silent_mutation Average:37.649; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N
vg1209679986 T -> DEL N N silent_mutation Average:37.649; most accessible tissue: Minghui63 young leaf, score: 50.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1209679986 3.85E-06 NA mr1010 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
vg1209679986 NA 6.80E-08 mr1425 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
vg1209679986 2.94E-07 NA mr1689 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
vg1209679986 NA 8.78E-06 mr1826 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
vg1209679986 NA 1.55E-07 mr1425_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
vg1209679986 NA 8.85E-08 mr1425_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