Search for Variation information by Variation ID:

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

Detailed information for vg1219583736:

Variant ID: vg1219583736 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 19583736
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, T: 0.44, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAGGTAGTAGTACTCCCTCCGTCCCAAAAAATACTCAATTCCTGGGTTTCCGTGTCTAACGTTTGACCGTCCATCTTATTTGAAAAAAATATGAAAAA[A/T]
TTTTAAAAAGATAAGTCATGCATAAAGTATTAATCATGTTTTATCATCTAACAATAATGAAAATACTAATCACAAAAAATTTTCATATAAAACGGACGGT

Reverse complement sequence

ACCGTCCGTTTTATATGAAAATTTTTTGTGATTAGTATTTTCATTATTGTTAGATGATAAAACATGATTAATACTTTATGCATGACTTATCTTTTTAAAA[T/A]
TTTTTCATATTTTTTTCAAATAAGATGGACGGTCAAACGTTAGACACGGAAACCCAGGAATTGAGTATTTTTTGGGACGGAGGGAGTACTACTACCTCTT

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 60.20% 34.60% 0.11% 5.14% NA
All Indica  2759 88.00% 3.40% 0.07% 8.59% NA
All Japonica  1512 7.00% 92.70% 0.20% 0.07% NA
Aus  269 97.80% 1.90% 0.00% 0.37% NA
Indica I  595 95.60% 2.50% 0.17% 1.68% NA
Indica II  465 80.20% 3.00% 0.00% 16.77% NA
Indica III  913 89.50% 1.80% 0.00% 8.76% NA
Indica Intermediate  786 85.00% 6.10% 0.13% 8.78% NA
Temperate Japonica  767 7.20% 92.40% 0.39% 0.00% NA
Tropical Japonica  504 3.60% 96.40% 0.00% 0.00% NA
Japonica Intermediate  241 13.70% 85.90% 0.00% 0.41% NA
VI/Aromatic  96 18.80% 81.20% 0.00% 0.00% NA
Intermediate  90 33.30% 62.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1219583736 A -> DEL N N silent_mutation Average:62.54; most accessible tissue: Minghui63 panicle, score: 92.078 N N N N
vg1219583736 A -> T LOC_Os12g32450.1 intron_variant ; MODIFIER silent_mutation Average:62.54; most accessible tissue: Minghui63 panicle, score: 92.078 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)
vg1219583736 A T -0.01 0.0 -0.01 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1219583736 NA 3.60E-14 mr1376 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
vg1219583736 NA 3.60E-14 mr1431 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
vg1219583736 NA 2.31E-14 mr1653 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
vg1219583736 NA 8.09E-06 mr1681 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
vg1219583736 NA 4.36E-11 mr1775 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
vg1219583736 NA 4.44E-07 mr1779 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
vg1219583736 NA 5.20E-09 mr1084_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
vg1219583736 NA 4.83E-12 mr1097_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
vg1219583736 NA 8.85E-13 mr1128_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
vg1219583736 NA 4.72E-39 mr1152_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
vg1219583736 NA 1.38E-08 mr1205_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
vg1219583736 NA 1.17E-19 mr1239_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
vg1219583736 NA 2.96E-07 mr1275_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
vg1219583736 1.58E-06 NA mr1350_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
vg1219583736 NA 6.99E-10 mr1506_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
vg1219583736 NA 7.11E-15 mr1575_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
vg1219583736 NA 6.06E-12 mr1636_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
vg1219583736 NA 7.43E-11 mr1646_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
vg1219583736 NA 2.68E-09 mr1681_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
vg1219583736 NA 5.20E-11 mr1830_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
vg1219583736 NA 4.52E-32 mr1873_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