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Detailed information for vg0819529346:

Variant ID: vg0819529346 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19529346
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGGAGCTGAAACCGTTTGGTTGAGCTCCAGCCCTAAAAGAGATGGAGTTGAAGTTAGAGCTGTGTCGAACAAGCTCTACATTAACACACCCGCAAATA[T/C]
ATACCCTCACCCTGATACATGTTAAAAGGGACGTAGGCCAGCAATAAATCCTTGGTCTCACTAATTTTCAATTAAAAACATGCTCGTGTGTACATAATAC

Reverse complement sequence

GTATTATGTACACACGAGCATGTTTTTAATTGAAAATTAGTGAGACCAAGGATTTATTGCTGGCCTACGTCCCTTTTAACATGTATCAGGGTGAGGGTAT[A/G]
TATTTGCGGGTGTGTTAATGTAGAGCTTGTTCGACACAGCTCTAACTTCAACTCCATCTCTTTTAGGGCTGGAGCTCAACCAAACGGTTTCAGCTCCACC

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 68.60% 31.20% 0.08% 0.08% NA
All Indica  2759 97.40% 2.50% 0.04% 0.11% NA
All Japonica  1512 16.10% 83.80% 0.00% 0.07% NA
Aus  269 77.00% 22.70% 0.37% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.80% 3.20% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.40% 0.13% 0.38% NA
Temperate Japonica  767 0.90% 99.00% 0.00% 0.13% NA
Tropical Japonica  504 40.30% 59.70% 0.00% 0.00% NA
Japonica Intermediate  241 14.10% 85.90% 0.00% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 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
vg0819529346 T -> C LOC_Os08g31560.1 downstream_gene_variant ; 567.0bp to feature; MODIFIER silent_mutation Average:88.197; most accessible tissue: Minghui63 young leaf, score: 94.489 N N N N
vg0819529346 T -> C LOC_Os08g31569.1 downstream_gene_variant ; 2662.0bp to feature; MODIFIER silent_mutation Average:88.197; most accessible tissue: Minghui63 young leaf, score: 94.489 N N N N
vg0819529346 T -> C LOC_Os08g31560-LOC_Os08g31569 intergenic_region ; MODIFIER silent_mutation Average:88.197; most accessible tissue: Minghui63 young leaf, score: 94.489 N N N N
vg0819529346 T -> DEL N N silent_mutation Average:88.197; most accessible tissue: Minghui63 young leaf, score: 94.489 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)
vg0819529346 T C 0.01 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819529346 NA 3.94E-06 mr1068_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
vg0819529346 NA 1.10E-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
vg0819529346 NA 8.24E-38 mr1224_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
vg0819529346 3.54E-06 NA mr1786_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
vg0819529346 NA 2.14E-06 mr1915_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