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Detailed information for vg0102400224:

Variant ID: vg0102400224 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2400224
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGGTCGATATCAAGAGGATGCAATGGACTTAACAGAGAAAGGAAACAAGCCAGATACATAGAATAGACGTAAGGGAGAGAATATAAACTTTCTATATT[C/T]
GGCCCAAACCTGAAAGGGAGGATTTTGATTCCTTTTTCCAATTAAATAATTGTTAAATGAGGTTTGTATTATTAAAATTAGCAATTAAGCTCTGAAAATT

Reverse complement sequence

AATTTTCAGAGCTTAATTGCTAATTTTAATAATACAAACCTCATTTAACAATTATTTAATTGGAAAAAGGAATCAAAATCCTCCCTTTCAGGTTTGGGCC[G/A]
AATATAGAAAGTTTATATTCTCTCCCTTACGTCTATTCTATGTATCTGGCTTGTTTCCTTTCTCTGTTAAGTCCATTGCATCCTCTTGATATCGACCACA

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 78.10% 0.90% 0.06% 20.88% NA
All Indica  2759 72.40% 0.00% 0.07% 27.55% NA
All Japonica  1512 83.70% 2.80% 0.07% 13.43% NA
Aus  269 94.10% 0.00% 0.00% 5.95% NA
Indica I  595 34.30% 0.00% 0.00% 65.71% NA
Indica II  465 94.40% 0.00% 0.00% 5.59% NA
Indica III  913 81.40% 0.00% 0.22% 18.40% NA
Indica Intermediate  786 77.70% 0.00% 0.00% 22.26% NA
Temperate Japonica  767 95.70% 0.10% 0.13% 4.04% NA
Tropical Japonica  504 74.20% 1.60% 0.00% 24.21% NA
Japonica Intermediate  241 65.10% 14.10% 0.00% 20.75% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 0.00% 0.00% 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
vg0102400224 C -> T LOC_Os01g05130.1 upstream_gene_variant ; 3046.0bp to feature; MODIFIER silent_mutation Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833 N N N N
vg0102400224 C -> T LOC_Os01g05105.1 downstream_gene_variant ; 1932.0bp to feature; MODIFIER silent_mutation Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833 N N N N
vg0102400224 C -> T LOC_Os01g05120.1 downstream_gene_variant ; 721.0bp to feature; MODIFIER silent_mutation Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833 N N N N
vg0102400224 C -> T LOC_Os01g05105-LOC_Os01g05120 intergenic_region ; MODIFIER silent_mutation Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833 N N N N
vg0102400224 C -> DEL N N silent_mutation Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833 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)
vg0102400224 C T -0.13 -0.13 -0.11 -0.1 -0.11 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102400224 NA 7.00E-06 mr1064 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
vg0102400224 NA 1.70E-06 mr1219 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
vg0102400224 9.09E-07 9.09E-07 mr1849 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
vg0102400224 NA 1.81E-06 mr1904 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