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Detailed information for vg1019343853:

Variant ID: vg1019343853 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19343853
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTTCCGCTATTTGCTGAAACATTGTTTTTATATAAGGTGAAACAACACCCGATTTAAACGAGTGAAACATTTTCGATCTACTTAGTACAACAATTCC[A/G]
ATATACCTGGTGGAACATCGTGTAACATTTAAAAATAATTCAATAATTAGGTAAAAAAAATTTCGTCGGAATATATCCATGTGTGGTCTTGTTTTGAAGA

Reverse complement sequence

TCTTCAAAACAAGACCACACATGGATATATTCCGACGAAATTTTTTTTACCTAATTATTGAATTATTTTTAAATGTTACACGATGTTCCACCAGGTATAT[T/C]
GGAATTGTTGTACTAAGTAGATCGAAAATGTTTCACTCGTTTAAATCGGGTGTTGTTTCACCTTATATAAAAACAATGTTTCAGCAAATAGCGGAAAAAT

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 67.90% 15.70% 12.97% 3.39% NA
All Indica  2759 48.40% 25.60% 20.66% 5.36% NA
All Japonica  1512 96.60% 1.50% 1.32% 0.60% NA
Aus  269 97.40% 1.10% 1.49% 0.00% NA
Indica I  595 69.90% 9.90% 17.48% 2.69% NA
Indica II  465 60.90% 18.50% 14.84% 5.81% NA
Indica III  913 22.70% 46.10% 23.99% 7.23% NA
Indica Intermediate  786 54.60% 17.80% 22.65% 4.96% NA
Temperate Japonica  767 99.50% 0.10% 0.26% 0.13% NA
Tropical Japonica  504 91.50% 4.20% 2.78% 1.59% NA
Japonica Intermediate  241 97.90% 0.40% 1.66% 0.00% NA
VI/Aromatic  96 90.60% 2.10% 7.29% 0.00% NA
Intermediate  90 73.30% 10.00% 13.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019343853 A -> G LOC_Os10g36180.1 upstream_gene_variant ; 2481.0bp to feature; MODIFIER silent_mutation Average:25.538; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1019343853 A -> G LOC_Os10g36170-LOC_Os10g36180 intergenic_region ; MODIFIER silent_mutation Average:25.538; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1019343853 A -> DEL N N silent_mutation Average:25.538; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1019343853 NA 1.49E-06 mr1038 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
vg1019343853 NA 8.16E-07 mr1058 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
vg1019343853 NA 4.23E-06 mr1179 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
vg1019343853 NA 1.28E-06 mr1252 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
vg1019343853 NA 4.90E-06 mr1432 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
vg1019343853 1.23E-07 3.82E-16 mr1713 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
vg1019343853 2.17E-06 1.45E-08 mr1713 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
vg1019343853 NA 1.17E-06 mr1729 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
vg1019343853 NA 2.89E-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
vg1019343853 NA 2.10E-07 mr1807 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
vg1019343853 NA 1.89E-06 mr1925 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
vg1019343853 NA 6.52E-08 mr1807_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