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Detailed information for vg0139781382:

Variant ID: vg0139781382 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39781382
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGCAGTAGTACACGTAACCTCGCACCTGCGAGCTTCCTAAAGCATGGTGTAAATTAACGGCGGGAAAGGGTTTTCTACTGGGAAACTATTTTCATCGAG[A/G]
GGATATCCTCTCGTTATTTATATATTACCCAAATAGCTATAAAAAATTGAAAAAATTTGAGAAGATGTATTAACATGTGATATATATATCACTCTACAAA

Reverse complement sequence

TTTGTAGAGTGATATATATATCACATGTTAATACATCTTCTCAAATTTTTTCAATTTTTTATAGCTATTTGGGTAATATATAAATAACGAGAGGATATCC[T/C]
CTCGATGAAAATAGTTTCCCAGTAGAAAACCCTTTCCCGCCGTTAATTTACACCATGCTTTAGGAAGCTCGCAGGTGCGAGGTTACGTGTACTACTGCCC

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 76.00% 20.70% 1.38% 1.90% NA
All Indica  2759 98.00% 1.40% 0.14% 0.43% NA
All Japonica  1512 31.50% 60.40% 3.97% 4.10% NA
Aus  269 97.40% 0.00% 0.00% 2.60% NA
Indica I  595 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.50% 0.40% 0.11% 0.99% NA
Indica Intermediate  786 96.90% 2.30% 0.38% 0.38% NA
Temperate Japonica  767 16.90% 75.70% 7.30% 0.00% NA
Tropical Japonica  504 43.70% 44.20% 0.60% 11.51% NA
Japonica Intermediate  241 52.30% 45.60% 0.41% 1.66% NA
VI/Aromatic  96 91.70% 1.00% 0.00% 7.29% NA
Intermediate  90 70.00% 26.70% 1.11% 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
vg0139781382 A -> G LOC_Os01g68440.1 downstream_gene_variant ; 4612.0bp to feature; MODIFIER silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 N N N N
vg0139781382 A -> G LOC_Os01g68450.1 downstream_gene_variant ; 1445.0bp to feature; MODIFIER silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 N N N N
vg0139781382 A -> G LOC_Os01g68440.3 downstream_gene_variant ; 4595.0bp to feature; MODIFIER silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 N N N N
vg0139781382 A -> G LOC_Os01g68450.2 downstream_gene_variant ; 1445.0bp to feature; MODIFIER silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 N N N N
vg0139781382 A -> G LOC_Os01g68460.1 intron_variant ; MODIFIER silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 N N N N
vg0139781382 A -> DEL N N silent_mutation Average:72.293; most accessible tissue: Minghui63 flag leaf, score: 92.792 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)
vg0139781382 A G 0.01 0.02 0.01 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139781382 NA 1.36E-13 mr1035_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
vg0139781382 NA 2.78E-07 mr1555_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
vg0139781382 NA 6.08E-07 mr1568_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
vg0139781382 NA 1.69E-08 mr1576_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
vg0139781382 NA 9.46E-06 mr1728_2 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
vg0139781382 NA 2.19E-07 mr1748_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
vg0139781382 NA 9.45E-08 mr1749_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
vg0139781382 3.94E-06 3.94E-06 mr1958_2 Jap_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