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Detailed information for vg0220789608:

Variant ID: vg0220789608 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20789608
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CCCTATATATTATTTATTTATAGGAGTCGTCAAATCTTCAGGCACTTATATGTCCTCATATCATATGTTTTTTCATTCATTTATTGTTCTTTCATCACAT[C/T]
ATGGTAAAAGAACCTACCTCTTCTTTCTTATATATCTTAAATTCTTAATCTTATAGGTTGTCGGACCATAACACATCAATGTCAATCAAAACAATGACAT

Reverse complement sequence

ATGTCATTGTTTTGATTGACATTGATGTGTTATGGTCCGACAACCTATAAGATTAAGAATTTAAGATATATAAGAAAGAAGAGGTAGGTTCTTTTACCAT[G/A]
ATGTGATGAAAGAACAATAAATGAATGAAAAAACATATGATATGAGGACATATAAGTGCCTGAAGATTTGACGACTCCTATAAATAAATAATATATAGGG

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 96.60% 3.10% 0.38% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 89.70% 9.10% 1.19% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 80.20% 17.50% 2.35% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0220789608 C -> T LOC_Os02g34650.1 upstream_gene_variant ; 3655.0bp to feature; MODIFIER silent_mutation Average:34.061; most accessible tissue: Callus, score: 51.318 N N N N
vg0220789608 C -> T LOC_Os02g34660.1 upstream_gene_variant ; 1958.0bp to feature; MODIFIER silent_mutation Average:34.061; most accessible tissue: Callus, score: 51.318 N N N N
vg0220789608 C -> T LOC_Os02g34650-LOC_Os02g34660 intergenic_region ; MODIFIER silent_mutation Average:34.061; most accessible tissue: Callus, score: 51.318 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220789608 NA 9.76E-06 mr1164_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
vg0220789608 NA 1.00E-06 mr1380_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
vg0220789608 1.90E-06 1.90E-06 mr1499_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
vg0220789608 NA 3.16E-06 mr1561_2 Jap_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
vg0220789608 1.54E-06 2.87E-08 mr1576_2 Jap_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