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Detailed information for vg0411081023:

Variant ID: vg0411081023 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11081023
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCCCTGCACCCGTATCCGCTCCACCTTCTTCGGTCGCTGGCTCCTTGCCCTGCTCTGCTGCCTCTACCTTCGCCAAGTGCTCGAGCAGGCGCGCCTTA[A/G]
CGGTAGATCGGCCCTCCTTTTGCCAGAACTGCTTGCGCCAGGCGCGTAAGGCGGGCGAAACGTCCTGAGAGCTGACTTCCCAATCCCCCTTCGTAAGCTT

Reverse complement sequence

AAGCTTACGAAGGGGGATTGGGAAGTCAGCTCTCAGGACGTTTCGCCCGCCTTACGCGCCTGGCGCAAGCAGTTCTGGCAAAAGGAGGGCCGATCTACCG[T/C]
TAAGGCGCGCCTGCTCGAGCACTTGGCGAAGGTAGAGGCAGCAGAGCAGGGCAAGGAGCCAGCGACCGAAGAAGGTGGAGCGGATACGGGTGCAGGGGCG

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 77.40% 21.80% 0.11% 0.72% NA
All Indica  2759 95.30% 3.70% 0.18% 0.76% NA
All Japonica  1512 39.00% 60.30% 0.00% 0.79% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 0.30% 0.00% 0.84% NA
Indica II  465 81.50% 17.60% 0.22% 0.65% NA
Indica III  913 99.20% 0.30% 0.22% 0.22% NA
Indica Intermediate  786 96.30% 2.00% 0.25% 1.40% NA
Temperate Japonica  767 4.00% 94.40% 0.00% 1.56% NA
Tropical Japonica  504 95.80% 4.20% 0.00% 0.00% NA
Japonica Intermediate  241 31.10% 68.90% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 82.20% 17.80% 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
vg0411081023 A -> DEL N N silent_mutation Average:65.385; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg0411081023 A -> G LOC_Os04g19870.1 upstream_gene_variant ; 458.0bp to feature; MODIFIER silent_mutation Average:65.385; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg0411081023 A -> G LOC_Os04g19880.1 upstream_gene_variant ; 4857.0bp to feature; MODIFIER silent_mutation Average:65.385; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg0411081023 A -> G LOC_Os04g19850.1 downstream_gene_variant ; 1465.0bp to feature; MODIFIER silent_mutation Average:65.385; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg0411081023 A -> G LOC_Os04g19850-LOC_Os04g19870 intergenic_region ; MODIFIER silent_mutation Average:65.385; most accessible tissue: Zhenshan97 young leaf, score: 88.995 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)
vg0411081023 A G 0.01 0.01 0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411081023 NA 5.65E-07 mr1040 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
vg0411081023 NA 7.41E-06 mr1077 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
vg0411081023 NA 2.89E-06 mr1121 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
vg0411081023 NA 2.29E-07 mr1194 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
vg0411081023 NA 3.43E-07 mr1206 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
vg0411081023 NA 5.59E-07 mr1252 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
vg0411081023 NA 5.79E-06 mr1330 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
vg0411081023 NA 1.78E-06 mr1629 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
vg0411081023 NA 1.10E-08 mr1658 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
vg0411081023 NA 2.97E-07 mr1715 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
vg0411081023 NA 3.61E-07 mr1739 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
vg0411081023 NA 1.41E-06 mr1826 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
vg0411081023 NA 1.72E-12 mr1844 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
vg0411081023 NA 4.56E-06 mr1844 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
vg0411081023 NA 1.38E-09 mr1880 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
vg0411081023 NA 3.86E-09 mr1378_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
vg0411081023 NA 5.70E-15 mr1520_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