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Detailed information for vg0617352597:

Variant ID: vg0617352597 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17352597
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTATTATAGACTTTGGTACCTGGGTACACGGTACCTTAGTACCGACTGGTACCTAGGTGTCACAAACTTTGGTACCTAGGTACCATGCCTAATACTTGT[G/A]
GGTACCAAGTCTGATATATGACGACTGATACCTAATGGAGAAGGCCATGGCACGGACACAGAAGGTCTCCTTGGCGACATGCGGTGGAGGTAGAGTAGGG

Reverse complement sequence

CCCTACTCTACCTCCACCGCATGTCGCCAAGGAGACCTTCTGTGTCCGTGCCATGGCCTTCTCCATTAGGTATCAGTCGTCATATATCAGACTTGGTACC[C/T]
ACAAGTATTAGGCATGGTACCTAGGTACCAAAGTTTGTGACACCTAGGTACCAGTCGGTACTAAGGTACCGTGTACCCAGGTACCAAAGTCTATAATACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.80% 30.60% 0.00% 0.57% NA
All Indica  2759 98.30% 1.60% 0.00% 0.11% NA
All Japonica  1512 10.10% 88.40% 0.00% 1.59% NA
Aus  269 88.80% 11.20% 0.00% 0.00% NA
Indica I  595 97.50% 2.40% 0.00% 0.17% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.10% 0.00% 0.25% NA
Temperate Japonica  767 3.70% 93.20% 0.00% 3.13% NA
Tropical Japonica  504 22.60% 77.40% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 0.00% 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
vg0617352597 G -> A LOC_Os06g30090.1 downstream_gene_variant ; 2444.0bp to feature; MODIFIER silent_mutation Average:90.575; most accessible tissue: Zhenshan97 young leaf, score: 95.694 N N N N
vg0617352597 G -> A LOC_Os06g30110.1 downstream_gene_variant ; 4849.0bp to feature; MODIFIER silent_mutation Average:90.575; most accessible tissue: Zhenshan97 young leaf, score: 95.694 N N N N
vg0617352597 G -> A LOC_Os06g30090-LOC_Os06g30110 intergenic_region ; MODIFIER silent_mutation Average:90.575; most accessible tissue: Zhenshan97 young leaf, score: 95.694 N N N N
vg0617352597 G -> DEL N N silent_mutation Average:90.575; most accessible tissue: Zhenshan97 young leaf, score: 95.694 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)
vg0617352597 G A -0.02 -0.03 -0.02 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617352597 NA 1.99E-76 mr1100 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
vg0617352597 1.90E-06 1.90E-06 mr1165 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
vg0617352597 NA 1.62E-10 mr1175 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
vg0617352597 NA 1.09E-07 mr1354 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
vg0617352597 NA 8.52E-38 mr1402 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
vg0617352597 NA 1.84E-20 mr1689 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
vg0617352597 7.86E-08 2.29E-10 mr1165_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
vg0617352597 NA 1.23E-29 mr1477_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
vg0617352597 NA 2.11E-17 mr1682_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
vg0617352597 2.71E-07 2.71E-07 mr1971_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