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Detailed information for vg1003484913:

Variant ID: vg1003484913 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3484913
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGATATAATGCTCGGGTAGATTAAATTGAAAACTTATGACAACAAAATATTTATACCCGCAAAATAGTTTGAATCGAAATTGGGTTTGCCTTAGTTCG[T/C]
GAATAATAAAGTTAATATAAAGAAATCGACTTTCGCATTCGACTTTCATTTGGATTTATTTGGATTTTTATTTGAATTCTAACCGAATTCAAATCAATTT

Reverse complement sequence

AAATTGATTTGAATTCGGTTAGAATTCAAATAAAAATCCAAATAAATCCAAATGAAAGTCGAATGCGAAAGTCGATTTCTTTATATTAACTTTATTATTC[A/G]
CGAACTAAGGCAAACCCAATTTCGATTCAAACTATTTTGCGGGTATAAATATTTTGTTGTCATAAGTTTTCAATTTAATCTACCCGAGCATTATATCCAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.00% 18.80% 3.20% 0.00% NA
All Indica  2759 83.90% 15.30% 0.80% 0.00% NA
All Japonica  1512 66.80% 30.20% 2.98% 0.00% NA
Aus  269 90.30% 0.00% 9.67% 0.00% NA
Indica I  595 80.00% 19.80% 0.17% 0.00% NA
Indica II  465 87.30% 12.70% 0.00% 0.00% NA
Indica III  913 83.50% 14.80% 1.75% 0.00% NA
Indica Intermediate  786 85.50% 13.90% 0.64% 0.00% NA
Temperate Japonica  767 58.10% 37.40% 4.43% 0.00% NA
Tropical Japonica  504 79.20% 20.00% 0.79% 0.00% NA
Japonica Intermediate  241 68.50% 28.60% 2.90% 0.00% NA
VI/Aromatic  96 45.80% 2.10% 52.08% 0.00% NA
Intermediate  90 82.20% 8.90% 8.89% 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
vg1003484913 T -> C LOC_Os10g06730.1 upstream_gene_variant ; 663.0bp to feature; MODIFIER silent_mutation Average:16.325; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 N N N N
vg1003484913 T -> C LOC_Os10g06730-LOC_Os10g06740 intergenic_region ; MODIFIER silent_mutation Average:16.325; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003484913 1.67E-06 1.14E-06 mr1547 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
vg1003484913 2.14E-06 5.04E-07 mr1547 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
vg1003484913 6.39E-10 5.79E-13 mr1709 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
vg1003484913 1.49E-07 3.20E-08 mr1709 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
vg1003484913 NA 1.50E-08 mr1709 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
vg1003484913 NA 5.68E-07 mr1831 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
vg1003484913 NA 4.03E-06 mr1409_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
vg1003484913 6.38E-08 8.62E-12 mr1547_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
vg1003484913 6.83E-07 1.17E-08 mr1547_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
vg1003484913 3.27E-06 3.27E-06 mr1547_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
vg1003484913 1.04E-12 1.06E-16 mr1709_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
vg1003484913 9.76E-09 8.76E-10 mr1709_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
vg1003484913 5.18E-09 1.59E-26 mr1709_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
vg1003484913 NA 9.65E-06 mr1765_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
vg1003484913 NA 1.67E-06 mr1922_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