Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0205347525:

Variant ID: vg0205347525 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5347525
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTGGTGGCGTCTCCTCTCTCTCTCTCTCTCTCTCTCTCACTCTCTCTCTTCAGGGGAAGGTGGGGGTGGGGGGAGAGAGAGACACTGATAAAAAAGAAA[G/T]
CCCCCGATGGCGACGGGGAAATTACCGGTTTGCCCCTCGCCTCGACGTGTATTTACGCCACGTGGTGGGGTTGTGGGCCGTTGGATCGTGGTTGGACGGA

Reverse complement sequence

TCCGTCCAACCACGATCCAACGGCCCACAACCCCACCACGTGGCGTAAATACACGTCGAGGCGAGGGGCAAACCGGTAATTTCCCCGTCGCCATCGGGGG[C/A]
TTTCTTTTTTATCAGTGTCTCTCTCTCCCCCCACCCCCACCTTCCCCTGAAGAGAGAGAGTGAGAGAGAGAGAGAGAGAGAGAGAGGAGACGCCACCACG

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 97.50% 2.30% 0.17% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 93.00% 6.60% 0.40% 0.00% NA
Aus  269 97.80% 1.90% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 81.20% 17.70% 1.19% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0205347525 G -> T LOC_Os02g10200.1 upstream_gene_variant ; 39.0bp to feature; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 N N N N
vg0205347525 G -> T LOC_Os02g10210.1 upstream_gene_variant ; 1195.0bp to feature; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 N N N N
vg0205347525 G -> T LOC_Os02g10220.1 upstream_gene_variant ; 3942.0bp to feature; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 N N N N
vg0205347525 G -> T LOC_Os02g10200.2 upstream_gene_variant ; 39.0bp to feature; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 N N N N
vg0205347525 G -> T LOC_Os02g10190.1 downstream_gene_variant ; 3007.0bp to feature; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 N N N N
vg0205347525 G -> T LOC_Os02g10200-LOC_Os02g10210 intergenic_region ; MODIFIER silent_mutation Average:99.562; most accessible tissue: Minghui63 root, score: 99.822 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)
vg0205347525 G T -0.05 -0.07 -0.05 -0.07 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205347525 1.44E-06 NA mr1042_2 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
vg0205347525 1.22E-06 NA mr1167_2 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
vg0205347525 NA 1.76E-06 mr1174_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
vg0205347525 NA 2.16E-07 mr1401_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
vg0205347525 7.10E-06 NA mr1502_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
vg0205347525 8.98E-06 NA mr1742_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
vg0205347525 7.49E-07 NA mr1871_2 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
vg0205347525 3.06E-06 NA mr1916_2 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
vg0205347525 4.48E-06 4.48E-06 mr1950_2 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