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Detailed information for vg0613465733:

Variant ID: vg0613465733 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13465733
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTAGGAATGCAAGCGGGGCGGACAAGCGGGTTTTTTTAGCCCACTTATCTCACTTTTTGTTTATTTTTCTTCTAAATTTTATACTATCGTGTAAAAAAT[A/G]
AACTAGCAAGCACGATTTTAAGCAGATAGTGAGACTACCCACTTGCATACATAGCCTTGCCTCCTCCCCTTGTATGCGCGCCACACGTTCATCCGCGCGG

Reverse complement sequence

CCGCGCGGATGAACGTGTGGCGCGCATACAAGGGGAGGAGGCAAGGCTATGTATGCAAGTGGGTAGTCTCACTATCTGCTTAAAATCGTGCTTGCTAGTT[T/C]
ATTTTTTACACGATAGTATAAAATTTAGAAGAAAAATAAACAAAAAGTGAGATAAGTGGGCTAAAAAAACCCGCTTGTCCGCCCCGCTTGCATTCCTAAG

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 69.00% 30.80% 0.13% 0.11% NA
All Indica  2759 97.30% 2.50% 0.07% 0.18% NA
All Japonica  1512 10.40% 89.50% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 97.10% 2.50% 0.17% 0.17% NA
Indica II  465 96.30% 3.00% 0.22% 0.43% NA
Indica III  913 99.20% 0.70% 0.00% 0.11% NA
Indica Intermediate  786 95.70% 4.20% 0.00% 0.13% NA
Temperate Japonica  767 3.80% 96.00% 0.26% 0.00% NA
Tropical Japonica  504 21.40% 78.60% 0.00% 0.00% NA
Japonica Intermediate  241 8.30% 91.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 62.20% 35.60% 2.22% 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
vg0613465733 A -> G LOC_Os06g23090.1 intron_variant ; MODIFIER silent_mutation Average:88.431; most accessible tissue: Callus, score: 96.6 N N N N
vg0613465733 A -> DEL N N silent_mutation Average:88.431; most accessible tissue: Callus, score: 96.6 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)
vg0613465733 A G -0.04 -0.03 -0.04 -0.04 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613465733 NA 1.29E-21 mr1020 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
vg0613465733 2.08E-27 2.76E-95 mr1033 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
vg0613465733 9.41E-15 2.44E-20 mr1033 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
vg0613465733 5.85E-18 7.94E-52 mr1176 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
vg0613465733 6.70E-10 3.45E-13 mr1176 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
vg0613465733 NA 1.19E-14 mr1276 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
vg0613465733 NA 1.57E-20 mr1477 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
vg0613465733 3.19E-10 6.93E-75 mr1536 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
vg0613465733 3.09E-09 3.09E-09 mr1536 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
vg0613465733 NA 5.04E-13 mr1740 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
vg0613465733 NA 5.69E-21 mr1971 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
vg0613465733 2.69E-36 1.06E-131 mr1033_2 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
vg0613465733 2.79E-18 1.03E-27 mr1033_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
vg0613465733 NA 1.16E-19 mr1276_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
vg0613465733 1.16E-12 2.37E-96 mr1536_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
vg0613465733 1.53E-10 3.70E-12 mr1536_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