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Detailed information for vg1126435712:

Variant ID: vg1126435712 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26435712
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, C: 0.29, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CAATTTCCAGACTACAGAATTAAGGTGATTAATCAACCTTTTCTGAACCTCCATGGATGTGTTTTCCGTTTCCTGCAACAGGATGAATGATTTAGTTTGC[G/C]
CAACTTAATATTGAATTGGCAAAGATGCAACACTGACAAGTACTGCAGATTACATGAACTATCCTTTTCTTGATCTTTGTAACAGTTACAGTTCACTGAA

Reverse complement sequence

TTCAGTGAACTGTAACTGTTACAAAGATCAAGAAAAGGATAGTTCATGTAATCTGCAGTACTTGTCAGTGTTGCATCTTTGCCAATTCAATATTAAGTTG[C/G]
GCAAACTAAATCATTCATCCTGTTGCAGGAAACGGAAAACACATCCATGGAGGTTCAGAAAAGGTTGATTAATCACCTTAATTCTGTAGTCTGGAAATTG

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 73.50% 26.50% 0.02% 0.00% NA
All Indica  2759 61.10% 38.80% 0.04% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 50.20% 49.80% 0.00% 0.00% NA
Indica I  595 55.50% 44.50% 0.00% 0.00% NA
Indica II  465 41.50% 58.30% 0.22% 0.00% NA
Indica III  913 68.30% 31.70% 0.00% 0.00% NA
Indica Intermediate  786 68.70% 31.30% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126435712 G -> C LOC_Os11g43760.1 intron_variant ; MODIFIER silent_mutation Average:51.723; most accessible tissue: Callus, score: 78.291 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126435712 NA 4.21E-07 mr1133 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
vg1126435712 NA 9.04E-09 mr1191 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
vg1126435712 2.79E-06 5.06E-13 mr1644 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
vg1126435712 NA 8.97E-06 mr1092_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
vg1126435712 NA 7.82E-07 mr1097_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
vg1126435712 NA 8.03E-06 mr1152_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
vg1126435712 1.30E-07 3.69E-15 mr1191_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
vg1126435712 NA 3.20E-07 mr1380_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
vg1126435712 NA 1.73E-06 mr1561_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
vg1126435712 NA 2.05E-06 mr1875_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
vg1126435712 NA 1.70E-06 mr1908_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