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Detailed information for vg0126202736:

Variant ID: vg0126202736 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 26202736
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTGTGGGCATTCGTCACTCGAGCCCACTTAACATTAACGAGCCACGCTTACGTTTCTTGGAGTATTTGCCTTTTTTGGGCCAACGCGAAAAAACACCG[C/T]
AGAGCCAATCCCAGTGGCCGCTTCGCCTTCGGGCCCGACGTCGAGCAGAAGCAAACGAAAGTGTAGGAAGAATGGTCTCCTCCACTTCCGGAGGAGGAGC

Reverse complement sequence

GCTCCTCCTCCGGAAGTGGAGGAGACCATTCTTCCTACACTTTCGTTTGCTTCTGCTCGACGTCGGGCCCGAAGGCGAAGCGGCCACTGGGATTGGCTCT[G/A]
CGGTGTTTTTTCGCGTTGGCCCAAAAAAGGCAAATACTCCAAGAAACGTAAGCGTGGCTCGTTAATGTTAAGTGGGCTCGAGTGACGAATGCCCACAGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.30% 3.30% 0.40% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 89.70% 9.30% 1.06% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.00% 0.91% 0.00% NA
Tropical Japonica  504 73.40% 25.20% 1.39% 0.00% NA
Japonica Intermediate  241 93.80% 5.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg0126202736 C -> T LOC_Os01g46090.1 upstream_gene_variant ; 479.0bp to feature; MODIFIER silent_mutation Average:89.135; most accessible tissue: Callus, score: 98.189 N N N N
vg0126202736 C -> T LOC_Os01g46080.1 downstream_gene_variant ; 1026.0bp to feature; MODIFIER silent_mutation Average:89.135; most accessible tissue: Callus, score: 98.189 N N N N
vg0126202736 C -> T LOC_Os01g46080.2 downstream_gene_variant ; 1026.0bp to feature; MODIFIER silent_mutation Average:89.135; most accessible tissue: Callus, score: 98.189 N N N N
vg0126202736 C -> T LOC_Os01g46080-LOC_Os01g46090 intergenic_region ; MODIFIER silent_mutation Average:89.135; most accessible tissue: Callus, score: 98.189 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)
vg0126202736 C T -0.05 -0.01 -0.04 -0.06 -0.06 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0126202736 NA 1.43E-06 mr1304 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
vg0126202736 NA 1.11E-07 mr1364 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
vg0126202736 NA 1.37E-07 mr1382 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
vg0126202736 NA 2.08E-07 mr1443 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
vg0126202736 NA 2.08E-06 mr1583 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
vg0126202736 NA 3.16E-10 mr1696 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
vg0126202736 6.50E-06 6.37E-07 mr1126_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
vg0126202736 NA 7.59E-07 mr1243_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
vg0126202736 NA 2.98E-06 mr1295_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
vg0126202736 NA 5.20E-06 mr1498_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