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Detailed information for vg0420365084:

Variant ID: vg0420365084 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20365084
Reference Allele: GAlternative Allele: A
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAATAATATGTTTTTATTGTTTTACTCACTGACATGTGGGTCCCATTTACATTTGTTTTTATTTTAGTGCTACGTAAGCGCCACGTCGATGCCACATG[G/A]
AAGTCAACCCGCCACGTAAGTGCCACGTAGGACAAAACCGCCTCCGAAACCGCCGAGGGAGGTGATTTGCTCTGGTTTTCAGAGAAGAATGAGGCGTTAT

Reverse complement sequence

ATAACGCCTCATTCTTCTCTGAAAACCAGAGCAAATCACCTCCCTCGGCGGTTTCGGAGGCGGTTTTGTCCTACGTGGCACTTACGTGGCGGGTTGACTT[C/T]
CATGTGGCATCGACGTGGCGCTTACGTAGCACTAAAATAAAAACAAATGTAAATGGGACCCACATGTCAGTGAGTAAAACAATAAAAACATATTATTGGG

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 93.70% 6.20% 0.15% 0.00% NA
All Indica  2759 98.30% 1.70% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 18.60% 79.60% 1.86% 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 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 95.30% 4.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 27.10% 1.04% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0420365084 G -> A LOC_Os04g33620.1 upstream_gene_variant ; 330.0bp to feature; MODIFIER silent_mutation Average:98.696; most accessible tissue: Minghui63 young leaf, score: 99.877 N N N N
vg0420365084 G -> A LOC_Os04g33630.1 upstream_gene_variant ; 527.0bp to feature; MODIFIER silent_mutation Average:98.696; most accessible tissue: Minghui63 young leaf, score: 99.877 N N N N
vg0420365084 G -> A LOC_Os04g33620-LOC_Os04g33630 intergenic_region ; MODIFIER silent_mutation Average:98.696; most accessible tissue: Minghui63 young leaf, score: 99.877 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)
vg0420365084 G A -0.02 -0.03 -0.02 -0.02 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420365084 NA 1.75E-07 mr1320 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
vg0420365084 NA 5.67E-06 mr1349 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
vg0420365084 NA 9.11E-09 mr1465 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
vg0420365084 NA 3.52E-06 mr1523 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
vg0420365084 NA 3.92E-06 mr1545 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
vg0420365084 1.26E-06 NA mr1216_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
vg0420365084 NA 6.62E-06 mr1740_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