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Detailed information for vg1206433093:

Variant ID: vg1206433093 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 6433093
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.33, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


AACAGACATAATGGTTGCACTCCCAGGGCTCACTACTACAAATATGATTTTTCCAAAGATCCAGGTATTATATTGATGGCAATGGGGTGTCCGATTTTCC[G/A]
TCAGGTGAAGATAATTATCGATCTGGAGAAAACTTGACACACACGATCTGCAAAATCCGAACCCTTCAATCGCAGCACTACGTCTTTTTTGGTTATCAAC

Reverse complement sequence

GTTGATAACCAAAAAAGACGTAGTGCTGCGATTGAAGGGTTCGGATTTTGCAGATCGTGTGTGTCAAGTTTTCTCCAGATCGATAATTATCTTCACCTGA[C/T]
GGAAAATCGGACACCCCATTGCCATCAATATAATACCTGGATCTTTGGAAAAATCATATTTGTAGTAGTGAGCCCTGGGAGTGCAACCATTATGTCTGTT

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 25.50% 15.90% 0.32% 58.32% NA
All Indica  2759 36.90% 7.20% 0.40% 55.49% NA
All Japonica  1512 5.80% 30.70% 0.20% 63.36% NA
Aus  269 1.50% 21.90% 0.37% 76.21% NA
Indica I  595 86.70% 4.20% 0.00% 9.08% NA
Indica II  465 20.60% 18.10% 1.08% 60.22% NA
Indica III  913 11.40% 2.70% 0.33% 85.54% NA
Indica Intermediate  786 38.30% 8.40% 0.38% 52.93% NA
Temperate Japonica  767 9.00% 40.00% 0.39% 50.59% NA
Tropical Japonica  504 2.20% 10.50% 0.00% 87.30% NA
Japonica Intermediate  241 2.90% 43.20% 0.00% 53.94% NA
VI/Aromatic  96 69.80% 10.40% 0.00% 19.79% NA
Intermediate  90 33.30% 18.90% 0.00% 47.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206433093 G -> DEL N N silent_mutation Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756 N N N N
vg1206433093 G -> A LOC_Os12g11840.1 downstream_gene_variant ; 3301.0bp to feature; MODIFIER silent_mutation Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756 N N N N
vg1206433093 G -> A LOC_Os12g11840-LOC_Os12g11860 intergenic_region ; MODIFIER silent_mutation Average:45.577; most accessible tissue: Zhenshan97 flower, score: 70.756 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1206433093 4.54E-06 NA mr1177 Jap_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
vg1206433093 7.55E-07 7.55E-07 mr1381 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
vg1206433093 NA 2.41E-08 mr1030_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
vg1206433093 NA 6.94E-06 mr1184_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
vg1206433093 NA 5.11E-06 mr1278_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
vg1206433093 NA 2.84E-06 mr1329_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
vg1206433093 NA 1.85E-06 mr1369_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
vg1206433093 NA 2.27E-07 mr1524_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
vg1206433093 1.14E-06 NA mr1549_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
vg1206433093 NA 5.48E-06 mr1652_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
vg1206433093 NA 6.51E-08 mr1683_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
vg1206433093 NA 1.37E-06 mr1687_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
vg1206433093 5.51E-06 1.12E-06 mr1923_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