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Detailed information for vg1216463799:

Variant ID: vg1216463799 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16463799
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.23, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:


CGGATCCCGAGCGGCGAGTCTATCGCCTTTCAGTATGCGTGGGACCACTACTTTCAGATGACTCCTGCTAGCGTCCAGGCCGATTGCTAGACATCTTGTT[C/T]
GTGGAAGTATGACTTTCAAGATTAATTGGTATGTAATTTTGTATTTCATGACAAAATAAATGGCCTGGTTTTAGTATGCTGCCAGGTGTGGTATATGTTT

Reverse complement sequence

AAACATATACCACACCTGGCAGCATACTAAAACCAGGCCATTTATTTTGTCATGAAATACAAAATTACATACCAATTAATCTTGAAAGTCATACTTCCAC[G/A]
AACAAGATGTCTAGCAATCGGCCTGGACGCTAGCAGGAGTCATCTGAAAGTAGTGGTCCCACGCATACTGAAAGGCGATAGACTCGCCGCTCGGGATCCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 47.70% 39.00% 0.36% 12.97% NA
All Indica  2759 64.90% 21.80% 0.36% 12.98% NA
All Japonica  1512 24.10% 67.30% 0.26% 8.33% NA
Aus  269 19.00% 54.30% 0.37% 26.39% NA
Indica I  595 90.30% 5.50% 0.17% 4.03% NA
Indica II  465 39.10% 51.80% 0.00% 9.03% NA
Indica III  913 68.10% 9.70% 0.44% 21.69% NA
Indica Intermediate  786 57.10% 30.30% 0.64% 11.96% NA
Temperate Japonica  767 13.00% 80.40% 0.26% 6.26% NA
Tropical Japonica  504 34.90% 55.40% 0.20% 9.52% NA
Japonica Intermediate  241 36.50% 50.60% 0.41% 12.45% NA
VI/Aromatic  96 15.60% 28.10% 1.04% 55.21% NA
Intermediate  90 37.80% 55.60% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216463799 C -> DEL N N silent_mutation Average:78.01; most accessible tissue: Minghui63 young leaf, score: 92.394 N N N N
vg1216463799 C -> T LOC_Os12g27930.1 3_prime_UTR_variant ; 11.0bp to feature; MODIFIER silent_mutation Average:78.01; most accessible tissue: Minghui63 young leaf, score: 92.394 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)
vg1216463799 C T 0.0 -0.06 -0.05 0.01 0.0 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216463799 NA 4.08E-06 mr1029 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
vg1216463799 NA 9.32E-09 mr1059 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
vg1216463799 NA 1.89E-10 mr1143 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
vg1216463799 NA 1.91E-10 mr1167 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
vg1216463799 NA 1.53E-06 mr1189 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
vg1216463799 NA 3.29E-11 mr1325 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
vg1216463799 NA 6.39E-07 mr1458 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
vg1216463799 1.81E-06 9.23E-08 mr1527 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
vg1216463799 NA 5.69E-06 mr1532 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
vg1216463799 NA 2.69E-10 mr1535 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
vg1216463799 NA 6.76E-06 mr1625 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
vg1216463799 NA 2.30E-10 mr1675 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
vg1216463799 NA 1.08E-06 mr1698 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
vg1216463799 NA 8.99E-09 mr1726 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
vg1216463799 NA 1.46E-07 mr1950 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
vg1216463799 NA 1.39E-09 mr1969 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
vg1216463799 NA 6.21E-11 mr1995 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
vg1216463799 NA 3.95E-06 mr1024_2 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
vg1216463799 NA 1.37E-06 mr1045_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
vg1216463799 NA 9.96E-06 mr1062_2 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
vg1216463799 NA 3.80E-07 mr1358_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
vg1216463799 NA 8.44E-07 mr1925_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