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Detailed information for vg0324608474:

Variant ID: vg0324608474 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24608474
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGGGTACTGGGCAGCACTTTAGAAGATGTAGCAGACTAGCAGTAGTAGCAGACTAGCACTTTCAACTCTCCCTCTCTCCTCCCTTTTTTTATTCCCCA[C/T]
CGGAGGAAGCCTCCTCTCTCTCCTCTATTTTCTTCCCCCACCGGAGGAACCGAGGCTGCCAGCGGGACAAAGACGAGCGGCGACGGAGGCGCTGGACGGC

Reverse complement sequence

GCCGTCCAGCGCCTCCGTCGCCGCTCGTCTTTGTCCCGCTGGCAGCCTCGGTTCCTCCGGTGGGGGAAGAAAATAGAGGAGAGAGAGGAGGCTTCCTCCG[G/A]
TGGGGAATAAAAAAAGGGAGGAGAGAGGGAGAGTTGAAAGTGCTAGTCTGCTACTACTGCTAGTCTGCTACATCTTCTAAAGTGCTGCCCAGTACCCACA

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 70.50% 5.60% 9.90% 14.01% NA
All Indica  2759 58.80% 5.90% 13.45% 21.78% NA
All Japonica  1512 96.50% 0.80% 2.51% 0.20% NA
Aus  269 64.30% 0.40% 17.10% 18.22% NA
Indica I  595 42.90% 18.00% 15.80% 23.36% NA
Indica II  465 50.80% 0.00% 20.22% 29.03% NA
Indica III  913 74.50% 1.20% 7.56% 16.76% NA
Indica Intermediate  786 57.50% 5.90% 14.50% 22.14% NA
Temperate Japonica  767 96.60% 0.10% 3.13% 0.13% NA
Tropical Japonica  504 98.00% 0.60% 1.19% 0.20% NA
Japonica Intermediate  241 92.90% 3.30% 3.32% 0.41% NA
VI/Aromatic  96 11.50% 84.40% 3.12% 1.04% NA
Intermediate  90 73.30% 6.70% 11.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0324608474 C -> T LOC_Os03g43870.1 downstream_gene_variant ; 966.0bp to feature; MODIFIER silent_mutation Average:87.418; most accessible tissue: Callus, score: 99.303 N N N N
vg0324608474 C -> T LOC_Os03g43860-LOC_Os03g43870 intergenic_region ; MODIFIER silent_mutation Average:87.418; most accessible tissue: Callus, score: 99.303 N N N N
vg0324608474 C -> DEL N N silent_mutation Average:87.418; most accessible tissue: Callus, score: 99.303 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)
vg0324608474 C T -0.09 -0.03 -0.04 -0.05 -0.07 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324608474 NA 8.81E-07 mr1860 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
vg0324608474 NA 8.51E-06 mr1138_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
vg0324608474 9.43E-06 NA mr1563_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
vg0324608474 2.38E-06 3.51E-10 mr1860_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