Search for Variation information by Variation ID:

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

Detailed information for vg1122900230:

Variant ID: vg1122900230 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22900230
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


TCATTTATAGCCAATCTAATAGCTCATTCATACAATAGTTTTATACTACACTATTAATACCTGGTCCCACCTGTCATACACACACTGCGTCTTGGAGTCC[G/A]
TGCTGCAGCTGACTATAAATCTGTAGTCCGCTGTTCTTCTCTTTTCTCATTTATCTTTTTAAAATATATTTGCAGCTGGCTTATAGCCTGCTACCTGCTC

Reverse complement sequence

GAGCAGGTAGCAGGCTATAAGCCAGCTGCAAATATATTTTAAAAAGATAAATGAGAAAAGAGAAGAACAGCGGACTACAGATTTATAGTCAGCTGCAGCA[C/T]
GGACTCCAAGACGCAGTGTGTGTATGACAGGTGGGACCAGGTATTAATAGTGTAGTATAAAACTATTGTATGAATGAGCTATTAGATTGGCTATAAATGA

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 73.10% 18.70% 0.04% 8.10% NA
All Indica  2759 69.60% 30.20% 0.04% 0.14% NA
All Japonica  1512 74.10% 1.10% 0.07% 24.74% NA
Aus  269 91.40% 7.80% 0.00% 0.74% NA
Indica I  595 17.50% 82.50% 0.00% 0.00% NA
Indica II  465 97.20% 2.60% 0.00% 0.22% NA
Indica III  913 88.00% 12.00% 0.00% 0.00% NA
Indica Intermediate  786 71.40% 28.10% 0.13% 0.38% NA
Temperate Japonica  767 81.20% 1.80% 0.00% 16.95% NA
Tropical Japonica  504 55.60% 0.20% 0.20% 44.05% NA
Japonica Intermediate  241 90.00% 0.80% 0.00% 9.13% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 87.80% 8.90% 0.00% 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
vg1122900230 G -> A LOC_Os11g38630.1 upstream_gene_variant ; 454.0bp to feature; MODIFIER silent_mutation Average:78.003; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg1122900230 G -> A LOC_Os11g38620-LOC_Os11g38630 intergenic_region ; MODIFIER silent_mutation Average:78.003; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N
vg1122900230 G -> DEL N N silent_mutation Average:78.003; most accessible tissue: Zhenshan97 panicle, score: 92.533 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122900230 NA 1.84E-06 mr1074 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
vg1122900230 NA 2.26E-06 mr1170 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
vg1122900230 NA 2.07E-10 mr1272 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
vg1122900230 NA 1.85E-06 mr1308 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
vg1122900230 NA 1.53E-06 mr1378 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
vg1122900230 NA 2.95E-08 mr1511 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
vg1122900230 NA 3.04E-07 mr1745 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
vg1122900230 NA 9.63E-06 mr1974 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
vg1122900230 NA 7.73E-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
vg1122900230 NA 1.60E-07 mr1557_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
vg1122900230 NA 3.47E-07 mr1805_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
vg1122900230 NA 6.43E-06 mr1923_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