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Detailed information for vg1124305277:

Variant ID: vg1124305277 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24305277
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ATAATAAAACATGATTAATACTTTATACGTGACTTATCTTTTTAATTTTTTTTAAATAAGACGGACGTTGGACACAAAAATTCAGGATTTTTTTCTTGAC[G/A,T]
GAGGGAGTACTGGTCACTGTATTCTGTTGAATGCAAGCCCGTCTCCTGCTCTCTTCTCTAACAACACTTTAGCAAAACTTTAAAAATACTTTTTTATAAA

Reverse complement sequence

TTTATAAAAAAGTATTTTTAAAGTTTTGCTAAAGTGTTGTTAGAGAAGAGAGCAGGAGACGGGCTTGCATTCAACAGAATACAGTGACCAGTACTCCCTC[C/T,A]
GTCAAGAAAAAAATCCTGAATTTTTGTGTCCAACGTCCGTCTTATTTAAAAAAAATTAAAAAGATAAGTCACGTATAAAGTATTAATCATGTTTTATTAT

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 64.70% 25.20% 3.07% 4.17% T: 2.86%
All Indica  2759 48.50% 37.30% 3.33% 6.85% T: 3.99%
All Japonica  1512 94.20% 2.10% 3.37% 0.20% T: 0.20%
Aus  269 66.20% 25.30% 0.37% 0.74% T: 7.43%
Indica I  595 60.80% 19.20% 6.89% 7.73% T: 5.38%
Indica II  465 46.90% 36.60% 3.01% 12.04% T: 1.51%
Indica III  913 41.40% 49.80% 1.10% 2.63% T: 5.04%
Indica Intermediate  786 48.50% 36.90% 3.44% 8.02% T: 3.18%
Temperate Japonica  767 91.90% 1.30% 6.39% 0.13% T: 0.26%
Tropical Japonica  504 96.20% 3.60% 0.00% 0.20% NA
Japonica Intermediate  241 97.10% 1.20% 0.83% 0.41% T: 0.41%
VI/Aromatic  96 49.00% 51.00% 0.00% 0.00% NA
Intermediate  90 76.70% 16.70% 1.11% 3.33% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124305277 G -> T LOC_Os11g40690.1 intron_variant ; MODIFIER silent_mutation Average:26.83; most accessible tissue: Callus, score: 61.881 N N N N
vg1124305277 G -> A LOC_Os11g40690.1 intron_variant ; MODIFIER silent_mutation Average:26.83; most accessible tissue: Callus, score: 61.881 N N N N
vg1124305277 G -> DEL N N silent_mutation Average:26.83; most accessible tissue: Callus, score: 61.881 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124305277 NA 2.85E-06 mr1309 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
vg1124305277 NA 2.54E-06 mr1115_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
vg1124305277 NA 2.53E-07 mr1205_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
vg1124305277 NA 1.02E-06 mr1205_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
vg1124305277 9.33E-06 1.97E-06 mr1209_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
vg1124305277 2.73E-06 2.72E-06 mr1209_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
vg1124305277 NA 1.80E-07 mr1238_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
vg1124305277 NA 2.73E-06 mr1376_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
vg1124305277 NA 2.20E-06 mr1431_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
vg1124305277 NA 3.42E-06 mr1484_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
vg1124305277 NA 3.22E-07 mr1566_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
vg1124305277 NA 1.65E-10 mr1609_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
vg1124305277 NA 8.03E-06 mr1735_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
vg1124305277 NA 2.13E-07 mr1795_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
vg1124305277 NA 2.24E-07 mr1900_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
vg1124305277 NA 1.31E-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