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Detailed information for vg0235531396:

Variant ID: vg0235531396 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35531396
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, G: 0.04, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGATAGCGTCACGAGCTTGTTACCCTGACATTTTGCAGTAATTGGAGTTTTCAAGAACAAAAGAAATGCAGCACGAAAATATGATAAATCCAGCTTTG[A/G]
CATTCTCTATAAGGAGTATATACCTCTAGATTCAATCTGAATAACTTGGAACAGCCAGCAAGTTCATCTGGCAGTACGGATATAGTGTTGTTTGACGCCT

Reverse complement sequence

AGGCGTCAAACAACACTATATCCGTACTGCCAGATGAACTTGCTGGCTGTTCCAAGTTATTCAGATTGAATCTAGAGGTATATACTCCTTATAGAGAATG[T/C]
CAAAGCTGGATTTATCATATTTTCGTGCTGCATTTCTTTTGTTCTTGAAAACTCCAATTACTGCAAAATGTCAGGGTAACAAGCTCGTGACGCTATCAGA

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 56.60% 43.20% 0.23% 0.00% NA
All Indica  2759 93.00% 6.70% 0.33% 0.00% NA
All Japonica  1512 4.20% 95.80% 0.07% 0.00% NA
Aus  269 1.90% 98.10% 0.00% 0.00% NA
Indica I  595 90.40% 9.10% 0.50% 0.00% NA
Indica II  465 95.50% 4.30% 0.22% 0.00% NA
Indica III  913 95.20% 4.50% 0.33% 0.00% NA
Indica Intermediate  786 91.00% 8.80% 0.25% 0.00% NA
Temperate Japonica  767 5.90% 94.00% 0.13% 0.00% NA
Tropical Japonica  504 2.40% 97.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 43.30% 55.60% 1.11% 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
vg0235531396 A -> G LOC_Os02g58040.1 downstream_gene_variant ; 2743.0bp to feature; MODIFIER silent_mutation Average:48.102; most accessible tissue: Zhenshan97 young leaf, score: 61.964 N N N N
vg0235531396 A -> G LOC_Os02g58030.1 intron_variant ; MODIFIER silent_mutation Average:48.102; most accessible tissue: Zhenshan97 young leaf, score: 61.964 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235531396 NA 1.86E-11 mr1316 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
vg0235531396 NA 1.56E-19 mr1580 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
vg0235531396 NA 8.99E-13 mr1655 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
vg0235531396 NA 2.77E-12 mr1657 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
vg0235531396 NA 4.30E-64 mr1970 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
vg0235531396 NA 2.45E-62 mr1078_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
vg0235531396 NA 2.93E-59 mr1090_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
vg0235531396 NA 5.05E-48 mr1094_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
vg0235531396 NA 4.34E-62 mr1096_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
vg0235531396 NA 1.25E-49 mr1111_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
vg0235531396 NA 1.78E-51 mr1121_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
vg0235531396 NA 2.93E-29 mr1270_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
vg0235531396 NA 8.52E-23 mr1316_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
vg0235531396 NA 7.08E-10 mr1649_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
vg0235531396 NA 3.33E-23 mr1877_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
vg0235531396 NA 2.03E-35 mr1932_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
vg0235531396 NA 3.20E-68 mr1970_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
vg0235531396 NA 3.75E-100 mr1973_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