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Detailed information for vg1110447272:

Variant ID: vg1110447272 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 10447272
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTCAGGGGGCGTACATCCCGTCCTGTCCAGTCAGTCATGATGATGAGAGGTCTTAGCCTCCCATCCCGGCCAGAGTCGGTTCATTCGCTCTGGTCAATT[A/G]
GGGTTCCCGTTTCCCAGTGCAACCAGGAGCCCAGAAGACTACACACCTTAAATGGTGGTTGACAGGGGCACCCCCCGTGTTAGGCGGCAAGATTTGGCAG

Reverse complement sequence

CTGCCAAATCTTGCCGCCTAACACGGGGGGTGCCCCTGTCAACCACCATTTAAGGTGTGTAGTCTTCTGGGCTCCTGGTTGCACTGGGAAACGGGAACCC[T/C]
AATTGACCAGAGCGAATGAACCGACTCTGGCCGGGATGGGAGGCTAAGACCTCTCATCATCATGACTGACTGGACAGGACGGGATGTACGCCCCCTGACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 4.80% 0.04% 1.46% NA
All Indica  2759 93.00% 6.40% 0.04% 0.54% NA
All Japonica  1512 99.70% 0.00% 0.00% 0.33% NA
Aus  269 84.40% 15.60% 0.00% 0.00% NA
Indica I  595 80.30% 19.50% 0.00% 0.17% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 96.20% 3.00% 0.00% 0.88% NA
Indica Intermediate  786 95.00% 4.10% 0.13% 0.76% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 98.30% 0.00% 0.00% 1.66% NA
VI/Aromatic  96 49.00% 1.00% 1.04% 48.96% NA
Intermediate  90 91.10% 6.70% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1110447272 A -> DEL N N silent_mutation Average:68.694; most accessible tissue: Zhenshan97 young leaf, score: 90.27 N N N N
vg1110447272 A -> G LOC_Os11g18530.1 downstream_gene_variant ; 812.0bp to feature; MODIFIER silent_mutation Average:68.694; most accessible tissue: Zhenshan97 young leaf, score: 90.27 N N N N
vg1110447272 A -> G LOC_Os11g18540.1 downstream_gene_variant ; 1580.0bp to feature; MODIFIER silent_mutation Average:68.694; most accessible tissue: Zhenshan97 young leaf, score: 90.27 N N N N
vg1110447272 A -> G LOC_Os11g18520-LOC_Os11g18530 intergenic_region ; MODIFIER silent_mutation Average:68.694; most accessible tissue: Zhenshan97 young leaf, score: 90.27 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)
vg1110447272 A G 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1110447272 8.60E-06 NA mr1154 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
vg1110447272 NA 5.01E-07 mr1739 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
vg1110447272 2.95E-08 NA mr1097_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
vg1110447272 1.20E-07 3.99E-08 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
vg1110447272 1.50E-06 NA mr1154_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
vg1110447272 1.21E-06 3.53E-06 mr1154_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
vg1110447272 NA 3.33E-06 mr1959_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