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Detailed information for vg0205107721:

Variant ID: vg0205107721 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5107721
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTAAAAGAGACCACTATAAAAGTTGTTATGAACTAAGGCCTGTTTGTTTCAACTTAAGATTATTGAGCCAGATTATTATAAGCTGGATTATAATAAGTC[G/A]
GCATAGAATAAATTGTTAGCTGTTTGTTTCTCTAGATTATTAGATGCTTGTTAGCTGTTAGCAACCCAATAATCTAAAAAAGCACCTTTAGAGTGGATTA

Reverse complement sequence

TAATCCACTCTAAAGGTGCTTTTTTAGATTATTGGGTTGCTAACAGCTAACAAGCATCTAATAATCTAGAGAAACAAACAGCTAACAATTTATTCTATGC[C/T]
GACTTATTATAATCCAGCTTATAATAATCTGGCTCAATAATCTTAAGTTGAAACAAACAGGCCTTAGTTCATAACAACTTTTATAGTGGTCTCTTTTAAA

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 91.10% 8.80% 0.02% 0.00% NA
All Indica  2759 93.90% 6.10% 0.04% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 28.60% 71.40% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 93.30% 6.70% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 8.00% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 62.50% 37.50% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0205107721 G -> A LOC_Os02g09880.1 upstream_gene_variant ; 4994.0bp to feature; MODIFIER silent_mutation Average:43.558; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N
vg0205107721 G -> A LOC_Os02g09870-LOC_Os02g09880 intergenic_region ; MODIFIER silent_mutation Average:43.558; most accessible tissue: Zhenshan97 panicle, score: 72.468 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205107721 NA 2.52E-06 mr1073 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
vg0205107721 NA 2.58E-09 mr1207 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
vg0205107721 NA 4.48E-06 mr1262 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
vg0205107721 NA 2.89E-06 mr1774 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
vg0205107721 NA 4.79E-06 mr1931 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