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Detailed information for vg0211103497:

Variant ID: vg0211103497 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11103497
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGATCCACCTCCACCGAGCCTGCGATGGCCTGATCCGCCACCGTAGGGTCCGCGATAGCCTGATCCGCCGCTGTAGGGCCCTCAACGGCCGGATCCGC[G/A]
GGCGGCGAGCAGATCCGCCTTCGTCGGCCTCGCGACAGGCATCGGGCGGCGGGCGTGCGCCGATAGCGAGTGGCGGGCGGCAGCGACAGATCACGCAGCG

Reverse complement sequence

CGCTGCGTGATCTGTCGCTGCCGCCCGCCACTCGCTATCGGCGCACGCCCGCCGCCCGATGCCTGTCGCGAGGCCGACGAAGGCGGATCTGCTCGCCGCC[C/T]
GCGGATCCGGCCGTTGAGGGCCCTACAGCGGCGGATCAGGCTATCGCGGACCCTACGGTGGCGGATCAGGCCATCGCAGGCTCGGTGGAGGTGGATCCGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.90% 8.00% 0.02% 0.11% NA
All Indica  2759 86.50% 13.30% 0.04% 0.18% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.30% 2.50% 0.00% 0.17% NA
Indica II  465 74.40% 24.70% 0.22% 0.65% NA
Indica III  913 81.40% 18.60% 0.00% 0.00% NA
Indica Intermediate  786 91.50% 8.40% 0.00% 0.13% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0211103497 G -> A LOC_Os02g19000.1 downstream_gene_variant ; 866.0bp to feature; MODIFIER silent_mutation Average:79.943; most accessible tissue: Minghui63 flag leaf, score: 92.302 N N N N
vg0211103497 G -> A LOC_Os02g19010.1 downstream_gene_variant ; 930.0bp to feature; MODIFIER silent_mutation Average:79.943; most accessible tissue: Minghui63 flag leaf, score: 92.302 N N N N
vg0211103497 G -> A LOC_Os02g19000-LOC_Os02g19010 intergenic_region ; MODIFIER silent_mutation Average:79.943; most accessible tissue: Minghui63 flag leaf, score: 92.302 N N N N
vg0211103497 G -> DEL N N silent_mutation Average:79.943; most accessible tissue: Minghui63 flag leaf, score: 92.302 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)
vg0211103497 G A -0.01 -0.01 -0.01 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211103497 4.20E-06 4.19E-06 mr1313 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
vg0211103497 NA 5.03E-06 mr1332_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
vg0211103497 NA 3.95E-06 mr1346_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