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Detailed information for vg1127691454:

Variant ID: vg1127691454 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27691454
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


ACGACCAGCTCCTTTCTATGGGCAGGAGCGAAGCACGCACATCTGTTGCATGGCTGCACAACGAGGAGATGCTCGATCTTGAGCATGACATTGAGGACTG[C/T]
GTCGACCGTTTCATGCACCTCCTCACCTGCAAGCATCATCGTGGTGGGGTGCGCCAGATGGCACATGAGGTAAAGATCCGCTCGAGCTTCAGTGAAGAGA

Reverse complement sequence

TCTCTTCACTGAAGCTCGAGCGGATCTTTACCTCATGTGCCATCTGGCGCACCCCACCACGATGATGCTTGCAGGTGAGGAGGTGCATGAAACGGTCGAC[G/A]
CAGTCCTCAATGTCATGCTCAAGATCGAGCATCTCCTCGTTGTGCAGCCATGCAACAGATGTGCGTGCTTCGCTCCTGCCCATAGAAAGGAGCTGGTCGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.50% 17.80% 0.44% 10.26% NA
All Indica  2759 67.80% 22.90% 0.29% 9.03% NA
All Japonica  1512 88.80% 3.00% 0.79% 7.41% NA
Aus  269 37.20% 23.80% 0.37% 38.66% NA
Indica I  595 73.10% 20.00% 0.00% 6.89% NA
Indica II  465 53.10% 36.80% 0.22% 9.89% NA
Indica III  913 75.60% 17.00% 0.55% 6.90% NA
Indica Intermediate  786 63.40% 23.80% 0.25% 12.60% NA
Temperate Japonica  767 94.40% 3.70% 0.52% 1.43% NA
Tropical Japonica  504 79.60% 1.60% 1.19% 17.66% NA
Japonica Intermediate  241 90.00% 4.10% 0.83% 4.98% NA
VI/Aromatic  96 6.20% 79.20% 0.00% 14.58% NA
Intermediate  90 70.00% 23.30% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127691454 C -> T LOC_Os11g45770.1 upstream_gene_variant ; 3427.0bp to feature; MODIFIER silent_mutation Average:73.855; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg1127691454 C -> T LOC_Os11g45750.2 upstream_gene_variant ; 1166.0bp to feature; MODIFIER silent_mutation Average:73.855; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg1127691454 C -> T LOC_Os11g45750.1 intron_variant ; MODIFIER silent_mutation Average:73.855; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N
vg1127691454 C -> DEL N N silent_mutation Average:73.855; most accessible tissue: Minghui63 flag leaf, score: 92.129 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1127691454 C T -0.02 0.0 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127691454 1.17E-06 7.09E-10 mr1662_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
vg1127691454 3.21E-06 6.55E-06 mr1662_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
vg1127691454 6.33E-06 NA mr1841_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
vg1127691454 NA 5.26E-06 mr1875_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
vg1127691454 NA 4.76E-06 mr1908_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