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Detailed information for vg0204904936:

Variant ID: vg0204904936 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4904936
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAAATCCACAGGAGCCTTTTCTTCCCGTTCTTTTTCCATCGGCAAAGTGCACAGATGCTTTCATCAAGACGACAACATCCCCGGTCCGGTTGTAACTC[G/A]
TAATCCATTTGTCCCATAAAAAACTAACCTATGCTAAATGTAACATATTCTAGTAATACGAATTTGGATATACCTATGTTCAGATTTATTGTACTAGAAT

Reverse complement sequence

ATTCTAGTACAATAAATCTGAACATAGGTATATCCAAATTCGTATTACTAGAATATGTTACATTTAGCATAGGTTAGTTTTTTATGGGACAAATGGATTA[C/T]
GAGTTACAACCGGACCGGGGATGTTGTCGTCTTGATGAAAGCATCTGTGCACTTTGCCGATGGAAAAAGAACGGGAAGAAAAGGCTCCTGTGGATTTTCT

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 68.10% 31.70% 0.19% 0.00% NA
All Indica  2759 68.20% 31.80% 0.04% 0.00% NA
All Japonica  1512 62.20% 37.20% 0.53% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 63.70% 36.30% 0.00% 0.00% NA
Indica II  465 72.00% 28.00% 0.00% 0.00% NA
Indica III  913 69.90% 30.00% 0.11% 0.00% NA
Indica Intermediate  786 67.40% 32.60% 0.00% 0.00% NA
Temperate Japonica  767 93.60% 5.60% 0.78% 0.00% NA
Tropical Japonica  504 9.50% 90.50% 0.00% 0.00% NA
Japonica Intermediate  241 72.60% 26.60% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0204904936 G -> A LOC_Os02g09520.1 upstream_gene_variant ; 2046.0bp to feature; MODIFIER silent_mutation Average:89.903; most accessible tissue: Minghui63 flower, score: 96.217 N N N N
vg0204904936 G -> A LOC_Os02g09530.1 downstream_gene_variant ; 3866.0bp to feature; MODIFIER silent_mutation Average:89.903; most accessible tissue: Minghui63 flower, score: 96.217 N N N N
vg0204904936 G -> A LOC_Os02g09510-LOC_Os02g09520 intergenic_region ; MODIFIER silent_mutation Average:89.903; most accessible tissue: Minghui63 flower, score: 96.217 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)
vg0204904936 G A -0.1 -0.12 -0.08 -0.01 -0.03 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0204904936 NA 5.68E-06 mr1087 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
vg0204904936 NA 6.57E-07 mr1090 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
vg0204904936 NA 9.77E-12 mr1241 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
vg0204904936 NA 8.82E-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
vg0204904936 NA 6.36E-07 mr1584 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
vg0204904936 NA 4.35E-06 mr1602 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
vg0204904936 NA 2.28E-07 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
vg0204904936 NA 1.16E-06 mr1671 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
vg0204904936 NA 3.11E-16 mr1789 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
vg0204904936 1.96E-06 NA mr1962 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
vg0204904936 NA 1.11E-06 mr1096_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
vg0204904936 4.24E-06 NA mr1613_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
vg0204904936 NA 4.10E-11 mr1789_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
vg0204904936 5.48E-06 NA mr1962_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