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Detailed information for vg0303832565:

Variant ID: vg0303832565 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 3832565
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGAGAGAGAGAGAGAGGGGGGGACTGAAATATGATTGTCAGCTTGGCAAAGAAAATGACACCGTAGCTGGTGTTACGGATTACTCCGTATTACATGGCTA[G/T]
ACTAAGGCCCTCTTTATTTAGGCTTATAAGCCAATTTATAAGTCGAAAAGTCTAAGCCAAAACAAACAATCAGCTTTTTTATTTGGCTTTTTTGAAGCCA

Reverse complement sequence

TGGCTTCAAAAAAGCCAAATAAAAAAGCTGATTGTTTGTTTTGGCTTAGACTTTTCGACTTATAAATTGGCTTATAAGCCTAAATAAAGAGGGCCTTAGT[C/A]
TAGCCATGTAATACGGAGTAATCCGTAACACCAGCTACGGTGTCATTTTCTTTGCCAAGCTGACAATCATATTTCAGTCCCCCCCTCTCTCTCTCTCTCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 6.90% 0.38% 0.00% NA
All Indica  2759 99.80% 0.10% 0.04% 0.00% NA
All Japonica  1512 82.30% 16.50% 1.12% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.40% 0.13% 0.00% NA
Temperate Japonica  767 85.80% 12.10% 2.09% 0.00% NA
Tropical Japonica  504 91.70% 8.30% 0.00% 0.00% NA
Japonica Intermediate  241 51.90% 47.70% 0.41% 0.00% NA
VI/Aromatic  96 33.30% 66.70% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0303832565 G -> T LOC_Os03g07530.1 upstream_gene_variant ; 1389.0bp to feature; MODIFIER silent_mutation Average:85.648; most accessible tissue: Minghui63 young leaf, score: 96.05 N N N N
vg0303832565 G -> T LOC_Os03g07530.2 upstream_gene_variant ; 1392.0bp to feature; MODIFIER silent_mutation Average:85.648; most accessible tissue: Minghui63 young leaf, score: 96.05 N N N N
vg0303832565 G -> T LOC_Os03g07530.3 upstream_gene_variant ; 1392.0bp to feature; MODIFIER silent_mutation Average:85.648; most accessible tissue: Minghui63 young leaf, score: 96.05 N N N N
vg0303832565 G -> T LOC_Os03g07510-LOC_Os03g07530 intergenic_region ; MODIFIER silent_mutation Average:85.648; most accessible tissue: Minghui63 young leaf, score: 96.05 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)
vg0303832565 G T -0.06 0.02 0.02 0.0 0.03 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0303832565 NA 4.16E-06 mr1123 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
vg0303832565 NA 2.90E-07 mr1180 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
vg0303832565 NA 2.98E-06 mr1183 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
vg0303832565 NA 4.00E-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
vg0303832565 1.02E-06 NA mr1117_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
vg0303832565 NA 1.12E-06 mr1117_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
vg0303832565 NA 4.64E-06 mr1119_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
vg0303832565 NA 4.33E-06 mr1123_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
vg0303832565 NA 4.16E-06 mr1149_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
vg0303832565 NA 2.85E-06 mr1240_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
vg0303832565 NA 3.67E-06 mr1496_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