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Detailed information for vg0510329960:

Variant ID: vg0510329960 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 10329960
Reference Allele: AAlternative Allele: C,T
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, C: 0.26, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTGATGAAGTGCGGAGTGATCTGTTCTCCCTGCAAACCTTGTTCCTTCAGTTTTAGCATGCGTTCCATCAATTCCACTGCCTGAGCAGCTTCATCTC[A/C,T]
CATAGGCAATGAGTTCCATGTGTCCTGGTAAACCGGAGGAAGACAGCAGTACTCAGGGAGTGCGGGCTCAGGATTTTGAACATAGAACCAGTTTACATGC

Reverse complement sequence

GCATGTAAACTGGTTCTATGTTCAAAATCCTGAGCCCGCACTCCCTGAGTACTGCTGTCTTCCTCCGGTTTACCAGGACACATGGAACTCATTGCCTATG[T/G,A]
GAGATGAAGCTGCTCAGGCAGTGGAATTGATGGAACGCATGCTAAAACTGAAGGAACAAGGTTTGCAGGGAGAACAGATCACTCCGCACTTCATCAAAAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.90% 3.00% 0.13% 0.00% NA
All Indica  2759 94.90% 5.00% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.10% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 91.60% 8.40% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 94.60% 5.30% 0.11% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0510329960 A -> T LOC_Os05g17960.1 downstream_gene_variant ; 2712.0bp to feature; MODIFIER N Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg0510329960 A -> T LOC_Os05g17980.1 downstream_gene_variant ; 2089.0bp to feature; MODIFIER N Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg0510329960 A -> T LOC_Os05g17970.1 intron_variant ; MODIFIER N Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg0510329960 A -> C LOC_Os05g17960.1 downstream_gene_variant ; 2712.0bp to feature; MODIFIER silent_mutation Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg0510329960 A -> C LOC_Os05g17980.1 downstream_gene_variant ; 2089.0bp to feature; MODIFIER silent_mutation Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N
vg0510329960 A -> C LOC_Os05g17970.1 intron_variant ; MODIFIER silent_mutation Average:36.599; most accessible tissue: Zhenshan97 flag leaf, score: 51.466 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0510329960 7.39E-07 7.39E-07 mr1460 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