Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1200312356:

Variant ID: vg1200312356 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 312356
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, A: 0.32, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAGGTCGTGAGTTCGATTCTCGCAACACCCCCTTAACGTTTTGCTATTTACAACTAGGTCCTTCTCTTACAGATGTGATGTACTCTTTCTGATGTTGC[A/T]
AGTCTCTGTCTTTTTCTCTTTCCTTTTTTTTGGTCCTGTACATGGTGCAAATTAGAAGCACTCCAAGATAATTGGCAGCTAAAATTGGGCCGTTTGCTAC

Reverse complement sequence

GTAGCAAACGGCCCAATTTTAGCTGCCAATTATCTTGGAGTGCTTCTAATTTGCACCATGTACAGGACCAAAAAAAAGGAAAGAGAAAAAGACAGAGACT[T/A]
GCAACATCAGAAAGAGTACATCACATCTGTAAGAGAAGGACCTAGTTGTAAATAGCAAAACGTTAAGGGGGTGTTGCGAGAATCGAACTCACGACCTCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.60% 45.10% 0.66% 1.61% NA
All Indica  2759 81.40% 17.80% 0.69% 0.11% NA
All Japonica  1512 4.00% 90.50% 0.66% 4.83% NA
Aus  269 54.30% 45.40% 0.37% 0.00% NA
Indica I  595 84.70% 14.60% 0.67% 0.00% NA
Indica II  465 82.80% 17.00% 0.22% 0.00% NA
Indica III  913 79.00% 19.90% 0.77% 0.33% NA
Indica Intermediate  786 81.00% 18.10% 0.89% 0.00% NA
Temperate Japonica  767 5.50% 83.80% 1.17% 9.52% NA
Tropical Japonica  504 2.40% 97.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 32.20% 66.70% 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
vg1200312356 A -> DEL N N silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01510.1 upstream_gene_variant ; 2110.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01510.2 upstream_gene_variant ; 2456.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01510.3 upstream_gene_variant ; 2110.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01510.4 upstream_gene_variant ; 1843.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01520.1 downstream_gene_variant ; 796.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01520.2 downstream_gene_variant ; 577.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01520.3 downstream_gene_variant ; 796.0bp to feature; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 N N N N
vg1200312356 A -> T LOC_Os12g01510-LOC_Os12g01520 intergenic_region ; MODIFIER silent_mutation Average:87.897; most accessible tissue: Zhenshan97 flower, score: 96.19 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)
vg1200312356 A T -0.04 -0.06 -0.04 0.0 -0.02 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200312356 NA 1.96E-09 mr1151 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
vg1200312356 NA 1.75E-06 mr1425 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
vg1200312356 5.89E-07 NA mr1425 Ind_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
vg1200312356 NA 8.65E-06 mr1450 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
vg1200312356 NA 4.67E-06 mr1626 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
vg1200312356 NA 2.06E-07 mr1850 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