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Detailed information for vg0420940131:

Variant ID: vg0420940131 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20940131
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CAAATGCCAAATTAATAACTTTTCCTACTAGTGATTAGATCCATTTTGGCAAAAAGTGCTTCGAAACAGCAAAACTTTTACCATTTGGAGGAACTAAACA[A/G]
GGCCTTAGAGGAAGAGATATCGCTCACAAATATCTTTTTTTTTTAAAAAAAAGAAGTTATGAGTGTGTTGGGATTGAATATAGAATCTCGGGGTTAAAAC

Reverse complement sequence

GTTTTAACCCCGAGATTCTATATTCAATCCCAACACACTCATAACTTCTTTTTTTTAAAAAAAAAAGATATTTGTGAGCGATATCTCTTCCTCTAAGGCC[T/C]
TGTTTAGTTCCTCCAAATGGTAAAAGTTTTGCTGTTTCGAAGCACTTTTTGCCAAAATGGATCTAATCACTAGTAGGAAAAGTTATTAATTTGGCATTTG

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 51.70% 47.70% 0.53% 0.06% NA
All Indica  2759 35.40% 64.20% 0.29% 0.07% NA
All Japonica  1512 85.90% 13.00% 1.06% 0.07% NA
Aus  269 22.70% 77.30% 0.00% 0.00% NA
Indica I  595 76.50% 23.20% 0.34% 0.00% NA
Indica II  465 12.90% 86.70% 0.43% 0.00% NA
Indica III  913 28.10% 71.70% 0.00% 0.11% NA
Indica Intermediate  786 26.10% 73.30% 0.51% 0.13% NA
Temperate Japonica  767 92.40% 5.60% 1.96% 0.00% NA
Tropical Japonica  504 75.60% 24.20% 0.20% 0.00% NA
Japonica Intermediate  241 86.70% 12.90% 0.00% 0.41% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 61.10% 37.80% 1.11% 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
vg0420940131 A -> DEL N N silent_mutation Average:78.461; most accessible tissue: Minghui63 young leaf, score: 97.74 N N N N
vg0420940131 A -> G LOC_Os04g34600.1 upstream_gene_variant ; 4079.0bp to feature; MODIFIER silent_mutation Average:78.461; most accessible tissue: Minghui63 young leaf, score: 97.74 N N N N
vg0420940131 A -> G LOC_Os04g34610.1 downstream_gene_variant ; 1220.0bp to feature; MODIFIER silent_mutation Average:78.461; most accessible tissue: Minghui63 young leaf, score: 97.74 N N N N
vg0420940131 A -> G LOC_Os04g34600-LOC_Os04g34610 intergenic_region ; MODIFIER silent_mutation Average:78.461; most accessible tissue: Minghui63 young leaf, score: 97.74 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)
vg0420940131 A G 0.0 0.03 0.04 0.06 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420940131 NA 2.22E-09 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0420940131 1.50E-06 1.50E-06 mr1098 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
vg0420940131 NA 5.91E-08 mr1659 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
vg0420940131 NA 5.92E-07 mr1861 Ind_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
vg0420940131 7.45E-06 7.45E-06 mr1883 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