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Detailed information for vg1219591736:

Variant ID: vg1219591736 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19591736
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAGATCAATACCTATAAATTTAATTTATTTTATTGATATATCAATTGTAATGATTACTTAGGACAACATTTTTTTAATAAAAAAACAAAAGTAACAAAT[G/C]
GAGCAGCGAAGGACATAGCTGCAATATATTTTCTTGTTAGTGGAGCTGCAGCTATGTTGTAGTTCGGGCATGTTAGTGGAGCTGCAGCTATGTTGTAGTT

Reverse complement sequence

AACTACAACATAGCTGCAGCTCCACTAACATGCCCGAACTACAACATAGCTGCAGCTCCACTAACAAGAAAATATATTGCAGCTATGTCCTTCGCTGCTC[C/G]
ATTTGTTACTTTTGTTTTTTTATTAAAAAAATGTTGTCCTAAGTAATCATTACAATTGATATATCAATAAAATAAATTAAATTTATAGGTATTGATCTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 36.40% 7.40% 2.01% 54.21% NA
All Indica  2759 4.20% 4.50% 1.01% 90.25% NA
All Japonica  1512 96.60% 0.90% 0.13% 2.31% NA
Aus  269 1.90% 71.00% 23.42% 3.72% NA
Indica I  595 3.70% 0.30% 0.17% 95.80% NA
Indica II  465 3.40% 2.20% 1.94% 92.47% NA
Indica III  913 2.40% 7.60% 0.44% 89.59% NA
Indica Intermediate  786 7.10% 5.60% 1.78% 85.50% NA
Temperate Japonica  767 98.00% 0.40% 0.13% 1.43% NA
Tropical Japonica  504 96.20% 0.40% 0.20% 3.17% NA
Japonica Intermediate  241 92.90% 3.70% 0.00% 3.32% NA
VI/Aromatic  96 82.30% 14.60% 0.00% 3.12% NA
Intermediate  90 63.30% 7.80% 2.22% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1219591736 G -> C LOC_Os12g32450-LOC_Os12g32470 intergenic_region ; MODIFIER silent_mutation Average:11.26; most accessible tissue: Callus, score: 48.032 N N N N
vg1219591736 G -> DEL N N silent_mutation Average:11.26; most accessible tissue: Callus, score: 48.032 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219591736 NA 8.44E-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
vg1219591736 NA 2.25E-06 mr1545 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
vg1219591736 NA 8.07E-06 mr1045_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
vg1219591736 NA 2.86E-10 mr1166_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
vg1219591736 3.71E-06 1.98E-06 mr1206_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
vg1219591736 3.33E-06 3.33E-06 mr1357_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
vg1219591736 3.20E-06 2.19E-06 mr1381_2 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
vg1219591736 NA 6.85E-06 mr1432_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
vg1219591736 7.89E-06 NA mr1730_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
vg1219591736 NA 1.66E-16 mr1846_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
vg1219591736 NA 7.61E-06 mr1901_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
vg1219591736 NA 5.11E-06 mr1906_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
vg1219591736 NA 1.13E-07 mr1909_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
vg1219591736 NA 5.54E-06 mr1909_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
vg1219591736 1.32E-06 1.32E-06 mr1941_2 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
vg1219591736 NA 4.96E-06 mr1943_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
vg1219591736 3.76E-06 3.76E-06 mr1953_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
vg1219591736 2.48E-06 1.65E-06 mr1980_2 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