Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1208187601:

Variant ID: vg1208187601 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8187601
Reference Allele: AAlternative Allele: G,T
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.57, A: 0.44, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGAGAAAGTTGCATAATATTTAACCTCTTGTATTGAGCTAATTATTTTATACATACCGCATATGTGTATCGTTGCATCTTATTTTCCCATAATCCTCC[A/G,T]
TAAGGATTAAACTTTGTTTGTATTGCACATTTGAATAAGTGATTATACATATTGCTCCTATACGTTGATTTATTTCTTATGTTCATAGTAGAACTTATGA

Reverse complement sequence

TCATAAGTTCTACTATGAACATAAGAAATAAATCAACGTATAGGAGCAATATGTATAATCACTTATTCAAATGTGCAATACAAACAAAGTTTAATCCTTA[T/C,A]
GGAGGATTATGGGAAAATAAGATGCAACGATACACATATGCGGTATGTATAAAATAATTAGCTCAATACAAGAGGTTAAATATTATGCAACTTTCTCTTG

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 48.90% 26.70% 0.40% 23.89% T: 0.08%
All Indica  2759 50.60% 37.20% 0.29% 11.78% T: 0.14%
All Japonica  1512 51.90% 4.90% 0.46% 42.79% NA
Aus  269 19.30% 30.50% 0.74% 49.44% NA
Indica I  595 38.50% 45.90% 0.34% 15.29% NA
Indica II  465 42.80% 50.10% 0.43% 6.67% NA
Indica III  913 61.00% 26.90% 0.11% 11.50% T: 0.44%
Indica Intermediate  786 52.20% 35.00% 0.38% 12.47% NA
Temperate Japonica  767 75.10% 6.90% 0.52% 17.47% NA
Tropical Japonica  504 23.20% 2.40% 0.60% 73.81% NA
Japonica Intermediate  241 37.80% 3.70% 0.00% 58.51% NA
VI/Aromatic  96 27.10% 64.60% 1.04% 7.29% NA
Intermediate  90 61.10% 18.90% 1.11% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208187601 A -> DEL N N silent_mutation Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1208187601 A -> G LOC_Os12g14360-LOC_Os12g14374 intergenic_region ; MODIFIER silent_mutation Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N
vg1208187601 A -> T LOC_Os12g14360-LOC_Os12g14374 intergenic_region ; MODIFIER silent_mutation Average:23.513; most accessible tissue: Zhenshan97 panicle, score: 32.308 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208187601 NA 7.80E-06 mr1037 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
vg1208187601 NA 2.99E-07 mr1049 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
vg1208187601 NA 8.97E-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
vg1208187601 NA 4.60E-09 mr1577 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
vg1208187601 NA 3.72E-07 mr1864_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