Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0232208358:

Variant ID: vg0232208358 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32208358
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTAGAAATTCGGATTTAATTACTAGGAATCTTATCCGTGTATTATATTTAATCATTTAGTCATAGACTAAATTAAATTGTATAATATTTCTAGGATTTC[G/A]
TCCGATATTTAGCTCGTAATAGAAATTTCTAACCTATTATATGGATATAATGCTCGGGGAGAGTAAATTAAAAACTTATGACAACGAAATAATTATACCC

Reverse complement sequence

GGGTATAATTATTTCGTTGTCATAAGTTTTTAATTTACTCTCCCCGAGCATTATATCCATATAATAGGTTAGAAATTTCTATTACGAGCTAAATATCGGA[C/T]
GAAATCCTAGAAATATTATACAATTTAATTTAGTCTATGACTAAATGATTAAATATAATACACGGATAAGATTCCTAGTAATTAAATCCGAATTTCTACC

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 73.90% 8.00% 7.89% 10.16% NA
All Indica  2759 66.20% 13.20% 11.05% 9.60% NA
All Japonica  1512 99.10% 0.10% 0.66% 0.20% NA
Aus  269 24.90% 4.50% 2.60% 68.03% NA
Indica I  595 62.70% 15.00% 17.65% 4.71% NA
Indica II  465 60.90% 4.90% 9.89% 24.30% NA
Indica III  913 76.80% 14.90% 3.29% 5.04% NA
Indica Intermediate  786 59.70% 14.60% 15.78% 9.92% NA
Temperate Japonica  767 99.50% 0.10% 0.26% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 0.00% 3.32% 0.83% NA
VI/Aromatic  96 29.20% 2.10% 46.88% 21.88% NA
Intermediate  90 82.20% 2.20% 6.67% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0232208358 G -> A LOC_Os02g52660.1 upstream_gene_variant ; 4789.0bp to feature; MODIFIER silent_mutation Average:12.336; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0232208358 G -> A LOC_Os02g52670.1 upstream_gene_variant ; 3023.0bp to feature; MODIFIER silent_mutation Average:12.336; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0232208358 G -> A LOC_Os02g52670-LOC_Os02g52680 intergenic_region ; MODIFIER silent_mutation Average:12.336; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N
vg0232208358 G -> DEL N N silent_mutation Average:12.336; most accessible tissue: Zhenshan97 panicle, score: 28.447 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232208358 NA 6.09E-08 mr1860 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
vg0232208358 4.69E-06 6.96E-07 mr1186_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
vg0232208358 NA 2.63E-07 mr1186_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
vg0232208358 2.69E-06 1.26E-06 mr1245_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
vg0232208358 NA 2.01E-06 mr1245_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
vg0232208358 NA 7.10E-06 mr1332_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
vg0232208358 NA 4.20E-06 mr1355_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
vg0232208358 4.52E-06 8.22E-09 mr1371_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
vg0232208358 NA 4.43E-06 mr1371_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
vg0232208358 NA 8.62E-06 mr1397_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
vg0232208358 5.31E-06 8.06E-07 mr1445_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
vg0232208358 NA 1.10E-06 mr1445_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
vg0232208358 NA 9.81E-07 mr1452_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
vg0232208358 NA 6.29E-06 mr1452_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
vg0232208358 NA 7.44E-06 mr1462_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
vg0232208358 NA 8.47E-06 mr1616_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
vg0232208358 NA 1.71E-07 mr1648_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
vg0232208358 NA 5.34E-07 mr1648_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
vg0232208358 5.91E-06 5.91E-06 mr1652_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
vg0232208358 4.50E-06 1.01E-09 mr1655_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
vg0232208358 NA 2.70E-06 mr1655_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
vg0232208358 5.29E-06 2.06E-08 mr1669_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
vg0232208358 NA 3.12E-06 mr1669_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
vg0232208358 NA 1.05E-06 mr1895_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
vg0232208358 NA 1.02E-06 mr1977_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
vg0232208358 NA 4.11E-06 mr1977_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
vg0232208358 4.43E-06 NA mr1982_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
vg0232208358 7.01E-06 7.01E-06 mr1982_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