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Detailed information for vg1126565937:

Variant ID: vg1126565937 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26565937
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.74, C: 0.27, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCTATCTCTTCTCTATCTTATATCTCCATCTCTATCTCTACTATTATAAAAATTGAAAATATTTTTGCCGGTACTTTGATACGTTATTCATGCATGAG[T/C]
CAGTTCTTAAGTTCGTTTGATTTTGGAATTATGGTTCCGTATTTGAGTCGGGCTTTAAGTTCGTTCGCTTTTCAAAATACAAAAGGAGTCATATAAGATA

Reverse complement sequence

TATCTTATATGACTCCTTTTGTATTTTGAAAAGCGAACGAACTTAAAGCCCGACTCAAATACGGAACCATAATTCCAAAATCAAACGAACTTAAGAACTG[A/G]
CTCATGCATGAATAACGTATCAAAGTACCGGCAAAAATATTTTCAATTTTTATAATAGTAGAGATAGAGATGGAGATATAAGATAGAGAAGAGATAGAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.70% 27.20% 0.13% 0.00% NA
All Indica  2759 59.00% 40.80% 0.18% 0.00% NA
All Japonica  1512 95.60% 4.40% 0.00% 0.00% NA
Aus  269 75.80% 24.20% 0.00% 0.00% NA
Indica I  595 87.20% 12.80% 0.00% 0.00% NA
Indica II  465 82.40% 17.60% 0.00% 0.00% NA
Indica III  913 26.60% 73.20% 0.22% 0.00% NA
Indica Intermediate  786 61.50% 38.20% 0.38% 0.00% NA
Temperate Japonica  767 96.10% 3.90% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg1126565937 T -> C LOC_Os11g43970.1 upstream_gene_variant ; 2596.0bp to feature; MODIFIER silent_mutation Average:73.536; most accessible tissue: Minghui63 root, score: 91.96 N N N N
vg1126565937 T -> C LOC_Os11g43970-LOC_Os11g43980 intergenic_region ; MODIFIER silent_mutation Average:73.536; most accessible tissue: Minghui63 root, score: 91.96 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126565937 NA 5.74E-11 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
vg1126565937 NA 7.27E-06 mr1538 Jap_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
vg1126565937 NA 4.99E-07 mr1662 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
vg1126565937 NA 2.59E-08 mr1662 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
vg1126565937 NA 7.08E-08 mr1667 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
vg1126565937 NA 3.60E-06 mr1980 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
vg1126565937 NA 6.47E-12 mr1133_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
vg1126565937 8.86E-06 2.10E-09 mr1517_2 Jap_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
vg1126565937 NA 2.16E-09 mr1538_2 Jap_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
vg1126565937 NA 1.83E-06 mr1662_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
vg1126565937 NA 2.67E-07 mr1662_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
vg1126565937 NA 1.65E-08 mr1667_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