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

Detailed information for vg0219709320:

Variant ID: vg0219709320 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19709320
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTCACTTTTAATGGTGGATTGTTTGACTTGCAATCTTAGTACTGGAGTGGAGTGAAGTGGATTGTTTGGCTTACAATCTTAGTACTGGACTACTAACC[G/A]
GAGTGGTTTATTATAGGCAGAGGTAGCTGTAGAAACGTATTATATACAGCTGCATGAGTAATGAGTATTAAATTACTGCCAAATATTTGATTTCGTTTCA

Reverse complement sequence

TGAAACGAAATCAAATATTTGGCAGTAATTTAATACTCATTACTCATGCAGCTGTATATAATACGTTTCTACAGCTACCTCTGCCTATAATAAACCACTC[C/T]
GGTTAGTAGTCCAGTACTAAGATTGTAAGCCAAACAATCCACTTCACTCCACTCCAGTACTAAGATTGCAAGTCAAACAATCCACCATTAAAAGTGACCA

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 94.80% 4.70% 0.53% 0.00% NA
All Indica  2759 91.60% 7.50% 0.91% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 1.30% 1.01% 0.00% NA
Indica II  465 74.40% 22.60% 3.01% 0.00% NA
Indica III  913 94.70% 5.00% 0.22% 0.00% NA
Indica Intermediate  786 93.60% 6.00% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0219709320 G -> A LOC_Os02g33130.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:79.496; most accessible tissue: Callus, score: 96.149 N N N N
vg0219709320 G -> A LOC_Os02g33130.1 5_prime_UTR_variant ; 125.0bp to feature; MODIFIER silent_mutation Average:79.496; most accessible tissue: Callus, score: 96.149 N N N N
vg0219709320 G -> A LOC_Os02g33140.1 downstream_gene_variant ; 980.0bp to feature; MODIFIER silent_mutation Average:79.496; most accessible tissue: Callus, score: 96.149 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219709320 NA 5.37E-06 mr1319 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
vg0219709320 NA 7.76E-06 mr1319 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
vg0219709320 4.53E-06 4.53E-06 mr1884 Ind_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