Search for Variation information by Variation ID:

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

Detailed information for vg0628275391:

Variant ID: vg0628275391 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 28275391
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGTTTAAGATTATTATAGTCTAGATTATTGAGCCAGATTACTATAAGCTGAATTATAATAAGCCGATATAGAATAAGCGGTTAGCTGTTTGTTTATCTG[G/A]
ATTATTAGCTGTTTGTTCGCGGTTAGCAACCCAACAATTTAAAAAAGCACATTTAGAGTGGATTATTAGATTATAATAATCTAACTTATAGATTATAATA

Reverse complement sequence

TATTATAATCTATAAGTTAGATTATTATAATCTAATAATCCACTCTAAATGTGCTTTTTTAAATTGTTGGGTTGCTAACCGCGAACAAACAGCTAATAAT[C/T]
CAGATAAACAAACAGCTAACCGCTTATTCTATATCGGCTTATTATAATTCAGCTTATAGTAATCTGGCTCAATAATCTAGACTATAATAATCTTAAACTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.90% 0.13% 0.00% NA
All Indica  2759 89.50% 10.30% 0.22% 0.00% NA
All Japonica  1512 3.00% 97.00% 0.00% 0.00% NA
Aus  269 29.00% 71.00% 0.00% 0.00% NA
Indica I  595 95.80% 3.70% 0.50% 0.00% NA
Indica II  465 79.60% 20.40% 0.00% 0.00% NA
Indica III  913 91.50% 8.40% 0.11% 0.00% NA
Indica Intermediate  786 88.40% 11.30% 0.25% 0.00% NA
Temperate Japonica  767 3.10% 96.90% 0.00% 0.00% NA
Tropical Japonica  504 3.60% 96.40% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0628275391 G -> A LOC_Os06g46560.1 upstream_gene_variant ; 2458.0bp to feature; MODIFIER silent_mutation Average:70.576; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0628275391 G -> A LOC_Os06g46570.1 upstream_gene_variant ; 252.0bp to feature; MODIFIER silent_mutation Average:70.576; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0628275391 G -> A LOC_Os06g46580.1 upstream_gene_variant ; 4958.0bp to feature; MODIFIER silent_mutation Average:70.576; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0628275391 G -> A LOC_Os06g46570.2 upstream_gene_variant ; 252.0bp to feature; MODIFIER silent_mutation Average:70.576; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N
vg0628275391 G -> A LOC_Os06g46560-LOC_Os06g46570 intergenic_region ; MODIFIER silent_mutation Average:70.576; most accessible tissue: Zhenshan97 panicle, score: 87.451 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628275391 NA 7.43E-06 mr1305 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
vg0628275391 NA 3.36E-18 mr1598 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
vg0628275391 NA 1.33E-06 mr1748 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
vg0628275391 NA 2.71E-17 mr1913 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
vg0628275391 NA 3.81E-06 mr1990 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
vg0628275391 NA 4.99E-10 mr1349_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