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Detailed information for vg0608024602:

Variant ID: vg0608024602 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8024602
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAACTTTTTATTTATATGATTTATTATTAAAAAATAATAACTTTTTATTTATATGATTTATAAGCGCTACTACTGTTGTCATGCACGTTCAAGTTTATAC[G/A]
ATGCAAACCACTATCTTCTCCTGTACGTACTAACATACACAGAAACACAAAAACAAAACAATAGCTTACGTACTGTTCGCCGGAAAGAAAAGAAAAAACC

Reverse complement sequence

GGTTTTTTCTTTTCTTTCCGGCGAACAGTACGTAAGCTATTGTTTTGTTTTTGTGTTTCTGTGTATGTTAGTACGTACAGGAGAAGATAGTGGTTTGCAT[C/T]
GTATAAACTTGAACGTGCATGACAACAGTAGTAGCGCTTATAAATCATATAAATAAAAAGTTATTATTTTTTAATAATAAATCATATAAATAAAAAGTTA

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 71.60% 28.30% 0.04% 0.00% NA
All Indica  2759 98.40% 1.60% 0.00% 0.00% NA
All Japonica  1512 21.60% 78.30% 0.07% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 35.60% 64.30% 0.13% 0.00% NA
Tropical Japonica  504 4.40% 95.60% 0.00% 0.00% NA
Japonica Intermediate  241 13.30% 86.70% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 67.80% 31.10% 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
vg0608024602 G -> A LOC_Os06g14379.1 downstream_gene_variant ; 4695.0bp to feature; MODIFIER silent_mutation Average:38.931; most accessible tissue: Zhenshan97 flower, score: 48.393 N N N N
vg0608024602 G -> A LOC_Os06g14379-LOC_Os06g14390 intergenic_region ; MODIFIER silent_mutation Average:38.931; most accessible tissue: Zhenshan97 flower, score: 48.393 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608024602 NA 7.18E-13 mr1521 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
vg0608024602 NA 3.84E-08 mr1604 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
vg0608024602 NA 3.43E-09 mr1776 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
vg0608024602 NA 3.89E-07 mr1779 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
vg0608024602 NA 1.96E-07 mr1810 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
vg0608024602 NA 5.65E-07 mr1824 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
vg0608024602 NA 9.99E-07 mr1886 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
vg0608024602 NA 5.71E-18 mr1281_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
vg0608024602 NA 3.47E-07 mr1408_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
vg0608024602 2.23E-07 NA mr1517_2 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
vg0608024602 2.43E-06 NA mr1517_2 Jap_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
vg0608024602 NA 5.03E-07 mr1568_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