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Detailed information for vg0419249774:

Variant ID: vg0419249774 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19249774
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTCTATATGAAAGTTGCTCTAAAATATCATATTAATATATTTTTTAAATTTGTAATAATTAAAACTCAATCAATTATACGTTAATACCACCTCGTTTT[G/A]
CGTAAAAAACTTAATCTTCAACTTCATCTTTATTTTCACGAGAAAAGAACACTTCAGAAAGTAGTCCAATTAAGGACACAAACGGCTAATCAGCTCCATC

Reverse complement sequence

GATGGAGCTGATTAGCCGTTTGTGTCCTTAATTGGACTACTTTCTGAAGTGTTCTTTTCTCGTGAAAATAAAGATGAAGTTGAAGATTAAGTTTTTTACG[C/T]
AAAACGAGGTGGTATTAACGTATAATTGATTGAGTTTTAATTATTACAAATTTAAAAAATATATTAATATGATATTTTAGAGCAACTTTCATATAGAAAG

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 59.10% 40.50% 0.42% 0.00% NA
All Indica  2759 34.30% 65.50% 0.18% 0.00% NA
All Japonica  1512 97.90% 1.10% 0.99% 0.00% NA
Aus  269 71.40% 28.60% 0.00% 0.00% NA
Indica I  595 21.00% 78.70% 0.34% 0.00% NA
Indica II  465 49.20% 50.80% 0.00% 0.00% NA
Indica III  913 36.60% 63.30% 0.11% 0.00% NA
Indica Intermediate  786 32.80% 66.90% 0.25% 0.00% NA
Temperate Japonica  767 96.20% 1.80% 1.96% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0419249774 G -> A LOC_Os04g32090.1 upstream_gene_variant ; 3803.0bp to feature; MODIFIER silent_mutation Average:73.746; most accessible tissue: Minghui63 root, score: 95.183 N N N N
vg0419249774 G -> A LOC_Os04g32090-LOC_Os04g32100 intergenic_region ; MODIFIER silent_mutation Average:73.746; most accessible tissue: Minghui63 root, score: 95.183 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)
vg0419249774 G A 0.01 0.0 -0.02 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419249774 NA 7.57E-13 mr1195 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
vg0419249774 1.98E-07 5.23E-11 mr1851 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
vg0419249774 8.13E-09 5.78E-11 mr1851 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
vg0419249774 4.95E-07 1.20E-13 mr1864 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
vg0419249774 1.62E-08 6.16E-12 mr1864 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
vg0419249774 NA 1.39E-18 mr1195_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
vg0419249774 NA 5.25E-16 mr1521_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
vg0419249774 NA 7.68E-06 mr1521_2 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
vg0419249774 NA 2.49E-09 mr1851_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