Search for Variation information by Variation ID:

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

Detailed information for vg0804660474:

Variant ID: vg0804660474 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 4660474
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCGCATGCGGCCGTCTTAAGTGACCGCATGCGAAGATCGATCTTCGCATGCGGCTGCGACGGCCGCATGCGCAAATGGTAATCTTCGCAGACCATTTC[G/A]
CGCATGCGGGCCGGCCAACCGCATGTGAAGATCGATTCCGCCCGTATGCAAAAACGCTTTCTGTAGTAGTGGTATGTACGATTACTTAAGAAACTAGTAA

Reverse complement sequence

TTACTAGTTTCTTAAGTAATCGTACATACCACTACTACAGAAAGCGTTTTTGCATACGGGCGGAATCGATCTTCACATGCGGTTGGCCGGCCCGCATGCG[C/T]
GAAATGGTCTGCGAAGATTACCATTTGCGCATGCGGCCGTCGCAGCCGCATGCGAAGATCGATCTTCGCATGCGGTCACTTAAGACGGCCGCATGCGAAA

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 62.40% 32.70% 4.95% 0.00% NA
All Indica  2759 89.50% 2.60% 7.90% 0.00% NA
All Japonica  1512 4.60% 94.80% 0.53% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 81.00% 5.50% 13.45% 0.00% NA
Indica II  465 81.10% 4.10% 14.84% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 88.80% 2.40% 8.78% 0.00% NA
Temperate Japonica  767 1.30% 97.90% 0.78% 0.00% NA
Tropical Japonica  504 11.10% 88.70% 0.20% 0.00% NA
Japonica Intermediate  241 1.70% 97.90% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 5.20% 1.04% 0.00% NA
Intermediate  90 63.30% 28.90% 7.78% 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
vg0804660474 G -> A LOC_Os08g08180.1 downstream_gene_variant ; 459.0bp to feature; MODIFIER silent_mutation Average:29.662; most accessible tissue: Callus, score: 55.279 N N N N
vg0804660474 G -> A LOC_Os08g08180-LOC_Os08g08190 intergenic_region ; MODIFIER silent_mutation Average:29.662; most accessible tissue: Callus, score: 55.279 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0804660474 NA 1.95E-13 mr1149 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
vg0804660474 NA 2.78E-07 mr1162 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
vg0804660474 NA 3.89E-32 mr1448 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
vg0804660474 NA 2.47E-23 mr1548 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
vg0804660474 NA 4.49E-24 mr1588 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
vg0804660474 NA 4.51E-07 mr1761 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
vg0804660474 NA 2.52E-07 mr1804 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
vg0804660474 1.19E-06 NA mr1865 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
vg0804660474 NA 2.47E-07 mr1915 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
vg0804660474 NA 1.18E-27 mr1588_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
vg0804660474 NA 2.09E-06 mr1588_2 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
vg0804660474 NA 8.53E-10 mr1761_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