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Detailed information for vg0625703169:

Variant ID: vg0625703169 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 25703169
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


AATTATATTAGTTATTAACAACAAATAAAATTAGTTTGACAGACTATGTTCTGAGATAAATACATTTAATAGACTATGTATGAGATTGTAGATGAAATAT[A/G]
CATGATATCCCGCACTTTGATTATATGCATGAATATATGTTAAGGATTATAAAAATATTGGATATATACATGTTAAAAATACTGTGAAAAATAATGTGAA

Reverse complement sequence

TTCACATTATTTTTCACAGTATTTTTAACATGTATATATCCAATATTTTTATAATCCTTAACATATATTCATGCATATAATCAAAGTGCGGGATATCATG[T/C]
ATATTTCATCTACAATCTCATACATAGTCTATTAAATGTATTTATCTCAGAACATAGTCTGTCAAACTAATTTTATTTGTTGTTAATAACTAATATAATT

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 66.50% 33.50% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 9.70% 90.30% 0.00% 0.00% NA
Aus  269 87.00% 13.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 5.00% 0.00% 0.00% NA
Temperate Japonica  767 14.60% 85.40% 0.00% 0.00% NA
Tropical Japonica  504 5.20% 94.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 21.90% 78.10% 0.00% 0.00% NA
Intermediate  90 56.70% 43.30% 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
vg0625703169 A -> G LOC_Os06g42740.1 upstream_gene_variant ; 872.0bp to feature; MODIFIER silent_mutation Average:60.547; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0625703169 A -> G LOC_Os06g42730.1 downstream_gene_variant ; 368.0bp to feature; MODIFIER silent_mutation Average:60.547; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N
vg0625703169 A -> G LOC_Os06g42730-LOC_Os06g42740 intergenic_region ; MODIFIER silent_mutation Average:60.547; most accessible tissue: Minghui63 panicle, score: 80.641 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0625703169 NA 7.40E-10 mr1097 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
vg0625703169 NA 9.69E-15 mr1118 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
vg0625703169 NA 1.39E-43 mr1152 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
vg0625703169 NA 8.54E-07 mr1245 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
vg0625703169 NA 1.52E-06 mr1278 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
vg0625703169 NA 1.62E-06 mr1315 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
vg0625703169 9.01E-07 NA mr1415 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
vg0625703169 9.01E-07 NA mr1567 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
vg0625703169 NA 1.32E-11 mr1751 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
vg0625703169 NA 4.60E-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
vg0625703169 NA 1.18E-06 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
vg0625703169 NA 6.48E-30 mr1922 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
vg0625703169 NA 2.38E-13 mr1940 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
vg0625703169 NA 4.79E-15 mr1118_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