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Detailed information for vg1125279847:

Variant ID: vg1125279847 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25279847
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


TTAAATTAATGTAAAACACCTAAACATTCACGCATGCATGTTATGGGTTTAATTACCGAGAATGCTGCAAATCTCTATATACGATTTCAGGGTCCGATCC[C/T]
GAGCCTCAGATAGGGCCACGTGGCATCAAGCGTTGCGCTCCATTCGAATTCTCGATGGAGAATGTGCCACGTATTCCCACCAATCCCAGGACCGTTAGAT

Reverse complement sequence

ATCTAACGGTCCTGGGATTGGTGGGAATACGTGGCACATTCTCCATCGAGAATTCGAATGGAGCGCAACGCTTGATGCCACGTGGCCCTATCTGAGGCTC[G/A]
GGATCGGACCCTGAAATCGTATATAGAGATTTGCAGCATTCTCGGTAATTAAACCCATAACATGCATGCGTGAATGTTTAGGTGTTTTACATTAATTTAA

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 42.90% 25.20% 1.44% 30.51% NA
All Indica  2759 36.80% 38.10% 2.14% 22.98% NA
All Japonica  1512 42.40% 7.90% 0.46% 49.21% NA
Aus  269 94.10% 0.00% 0.37% 5.58% NA
Indica I  595 14.50% 36.10% 0.84% 48.57% NA
Indica II  465 48.80% 22.60% 0.65% 27.96% NA
Indica III  913 44.00% 41.70% 4.82% 9.42% NA
Indica Intermediate  786 38.00% 44.70% 0.89% 16.41% NA
Temperate Japonica  767 55.70% 2.10% 0.52% 41.72% NA
Tropical Japonica  504 25.20% 17.30% 0.20% 57.34% NA
Japonica Intermediate  241 36.10% 7.10% 0.83% 56.02% NA
VI/Aromatic  96 82.30% 0.00% 0.00% 17.71% NA
Intermediate  90 43.30% 20.00% 1.11% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125279847 C -> T LOC_Os11g42030.1 downstream_gene_variant ; 1112.0bp to feature; MODIFIER silent_mutation Average:96.798; most accessible tissue: Zhenshan97 flag leaf, score: 98.64 N N N N
vg1125279847 C -> T LOC_Os11g42030-LOC_Os11g42040 intergenic_region ; MODIFIER silent_mutation Average:96.798; most accessible tissue: Zhenshan97 flag leaf, score: 98.64 N N N N
vg1125279847 C -> DEL N N silent_mutation Average:96.798; most accessible tissue: Zhenshan97 flag leaf, score: 98.64 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)
vg1125279847 C T 0.04 0.16 0.2 0.02 0.07 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125279847 NA 5.92E-09 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
vg1125279847 3.73E-06 1.10E-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
vg1125279847 NA 4.38E-06 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
vg1125279847 3.79E-06 3.79E-06 mr1796 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
vg1125279847 NA 4.14E-06 mr1990 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
vg1125279847 NA 2.42E-08 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
vg1125279847 NA 8.93E-07 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
vg1125279847 NA 1.70E-06 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
vg1125279847 NA 7.13E-06 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