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Detailed information for vg0423794940:

Variant ID: vg0423794940 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 23794940
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAAGACAATGAGATAGTTATTTAATAAATTTTAAGTAAAATCATACTTTAAAAATAGATTTTGTTTAGGTGCTAGCCGCGCAATTGCGCGGGCCACCCA[G/A]
CTAGTTTTGCAAAAGAAGAGGTGTTCGTAAATTTGTCCAAGTAAATGTGCTAAGTTATCCCTATTTGTTTATGTACTTCCTCCGTTTCACAATGTAAGTC

Reverse complement sequence

GACTTACATTGTGAAACGGAGGAAGTACATAAACAAATAGGGATAACTTAGCACATTTACTTGGACAAATTTACGAACACCTCTTCTTTTGCAAAACTAG[C/T]
TGGGTGGCCCGCGCAATTGCGCGGCTAGCACCTAAACAAAATCTATTTTTAAAGTATGATTTTACTTAAAATTTATTAAATAACTATCTCATTGTCTTAA

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 93.10% 6.90% 0.04% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 91.10% 8.70% 0.13% 0.00% NA
Aus  269 46.10% 53.90% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 76.20% 23.40% 0.40% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0423794940 G -> A LOC_Os04g39970.1 upstream_gene_variant ; 2069.0bp to feature; MODIFIER silent_mutation Average:60.095; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N
vg0423794940 G -> A LOC_Os04g39960.1 downstream_gene_variant ; 4671.0bp to feature; MODIFIER silent_mutation Average:60.095; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N
vg0423794940 G -> A LOC_Os04g39980.1 downstream_gene_variant ; 469.0bp to feature; MODIFIER silent_mutation Average:60.095; most accessible tissue: Zhenshan97 flower, score: 92.326 N N N N
vg0423794940 G -> A LOC_Os04g39970-LOC_Os04g39980 intergenic_region ; MODIFIER silent_mutation Average:60.095; most accessible tissue: Zhenshan97 flower, score: 92.326 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)
vg0423794940 G A -0.01 0.0 -0.02 -0.01 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0423794940 NA 1.43E-08 mr1073 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
vg0423794940 NA 7.44E-06 mr1073 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
vg0423794940 NA 1.68E-06 mr1345 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
vg0423794940 NA 9.46E-07 mr1365 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
vg0423794940 NA 3.35E-07 mr1382 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
vg0423794940 NA 2.05E-06 mr1583 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
vg0423794940 NA 1.00E-12 mr1696 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
vg0423794940 NA 3.54E-08 mr1762 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
vg0423794940 1.95E-06 4.75E-09 mr1852 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
vg0423794940 NA 4.47E-10 mr1852 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
vg0423794940 NA 2.51E-06 mr1263_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
vg0423794940 NA 5.78E-06 mr1729_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