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Detailed information for vg0233489978:

Variant ID: vg0233489978 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33489978
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACTTTCGTCTCTTAACTGCAAAACCGGGTATGACCCGTCCCTCAACTTACGAAAACCGGGCAAACAAGATCCCTCGGTCAGTCCGGTTTTGGCCGACGTG[A/G]
CGCCTACATGGCTTCTTTGACTTGGTCTTCATCTCATGTGACATTGACGTGACGCTTAGGTGGCAATTTTATATCTCAAAAAATAATAAAAATCGTGGGA

Reverse complement sequence

TCCCACGATTTTTATTATTTTTTGAGATATAAAATTGCCACCTAAGCGTCACGTCAATGTCACATGAGATGAAGACCAAGTCAAAGAAGCCATGTAGGCG[T/C]
CACGTCGGCCAAAACCGGACTGACCGAGGGATCTTGTTTGCCCGGTTTTCGTAAGTTGAGGGACGGGTCATACCCGGTTTTGCAGTTAAGAGACGAAAGT

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 88.30% 9.30% 2.41% 0.00% NA
All Indica  2759 99.60% 0.30% 0.11% 0.00% NA
All Japonica  1512 64.90% 27.90% 7.14% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 0.80% 0.38% 0.00% NA
Temperate Japonica  767 38.10% 50.50% 11.47% 0.00% NA
Tropical Japonica  504 97.40% 1.20% 1.39% 0.00% NA
Japonica Intermediate  241 82.60% 12.00% 5.39% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 84.40% 13.30% 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
vg0233489978 A -> G LOC_Os02g54690.1 upstream_gene_variant ; 1637.0bp to feature; MODIFIER silent_mutation Average:99.672; most accessible tissue: Zhenshan97 flower, score: 99.918 N N N N
vg0233489978 A -> G LOC_Os02g54700.2 upstream_gene_variant ; 3443.0bp to feature; MODIFIER silent_mutation Average:99.672; most accessible tissue: Zhenshan97 flower, score: 99.918 N N N N
vg0233489978 A -> G LOC_Os02g54670.1 downstream_gene_variant ; 1479.0bp to feature; MODIFIER silent_mutation Average:99.672; most accessible tissue: Zhenshan97 flower, score: 99.918 N N N N
vg0233489978 A -> G LOC_Os02g54680.1 downstream_gene_variant ; 521.0bp to feature; MODIFIER silent_mutation Average:99.672; most accessible tissue: Zhenshan97 flower, score: 99.918 N N N N
vg0233489978 A -> G LOC_Os02g54680-LOC_Os02g54690 intergenic_region ; MODIFIER silent_mutation Average:99.672; most accessible tissue: Zhenshan97 flower, score: 99.918 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)
vg0233489978 A G 0.01 0.02 0.02 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233489978 NA 4.80E-06 mr1503 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
vg0233489978 2.67E-06 6.04E-15 mr1712 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
vg0233489978 NA 2.86E-06 mr1712 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
vg0233489978 NA 4.65E-06 mr1910 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
vg0233489978 NA 3.97E-09 mr1977 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
vg0233489978 NA 4.01E-06 mr1627_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
vg0233489978 3.20E-06 NA mr1768_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
vg0233489978 NA 5.13E-06 mr1768_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
vg0233489978 NA 8.26E-07 mr1977_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