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Detailed information for vg0116423916:

Variant ID: vg0116423916 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16423916
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCATTCTCCAGTATTCGGCAGGCTACATCCCACCCCAGGTCTACCCGCAAGTGCCGATTCAAGCCCTTCCGTCACAAGTCATGCAAGCACCAGCGTACTT[C/T]
GCCGGACAGCCTTCGACCGCCACAGTACATCCGACCCCTCATGTACAGTCACAAGTTCGGCCGGTCGCTGCCCAAGTATGCCCCCCGCCACCTGGTCAAA

Reverse complement sequence

TTTGACCAGGTGGCGGGGGGCATACTTGGGCAGCGACCGGCCGAACTTGTGACTGTACATGAGGGGTCGGATGTACTGTGGCGGTCGAAGGCTGTCCGGC[G/A]
AAGTACGCTGGTGCTTGCATGACTTGTGACGGAAGGGCTTGAATCGGCACTTGCGGGTAGACCTGGGGTGGGATGTAGCCTGCCGAATACTGGAGAATGG

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 81.10% 1.40% 8.53% 9.04% NA
All Indica  2759 70.20% 2.30% 12.79% 14.64% NA
All Japonica  1512 96.30% 0.00% 2.58% 1.12% NA
Aus  269 97.00% 0.00% 1.86% 1.12% NA
Indica I  595 80.70% 0.00% 12.61% 6.72% NA
Indica II  465 50.10% 10.80% 15.05% 24.09% NA
Indica III  913 70.30% 0.20% 13.47% 15.99% NA
Indica Intermediate  786 74.20% 1.50% 10.81% 13.49% NA
Temperate Japonica  767 98.70% 0.00% 1.17% 0.13% NA
Tropical Japonica  504 92.50% 0.00% 4.76% 2.78% NA
Japonica Intermediate  241 96.70% 0.00% 2.49% 0.83% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 91.10% 0.00% 5.56% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0116423916 C -> T LOC_Os01g29310.1 upstream_gene_variant ; 427.0bp to feature; MODIFIER silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 N N N N
vg0116423916 C -> T LOC_Os01g29320.1 upstream_gene_variant ; 1867.0bp to feature; MODIFIER silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 N N N N
vg0116423916 C -> T LOC_Os01g29290.1 downstream_gene_variant ; 4287.0bp to feature; MODIFIER silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 N N N N
vg0116423916 C -> T LOC_Os01g29300.1 downstream_gene_variant ; 876.0bp to feature; MODIFIER silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 N N N N
vg0116423916 C -> T LOC_Os01g29300-LOC_Os01g29310 intergenic_region ; MODIFIER silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 N N N N
vg0116423916 C -> DEL N N silent_mutation Average:71.703; most accessible tissue: Minghui63 flag leaf, score: 87.854 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)
vg0116423916 C T -0.01 -0.01 -0.01 -0.01 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116423916 7.89E-07 1.81E-08 mr1893_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