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Detailed information for vg1217949602:

Variant ID: vg1217949602 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17949602
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAAATTTTTTATAATTAGTATTTTTATTGTTGTTAGATGATAAAACATGATGAATACTTTATGCTGACTTATCTTTTTAATTTTTTTCATAATTTTTT[T/C]
AAATAAGATGGACGGTTAAATATTGGACACGGATATCAGGGTTTGTCTTTTTTTTTTTTTTTTTTTTTTGACTGAGGAAGTATGTCCTGTGGTACCCCTG

Reverse complement sequence

CAGGGGTACCACAGGACATACTTCCTCAGTCAAAAAAAAAAAAAAAAAAAAAAGACAAACCCTGATATCCGTGTCCAATATTTAACCGTCCATCTTATTT[A/G]
AAAAAATTATGAAAAAAATTAAAAAGATAAGTCAGCATAAAGTATTCATCATGTTTTATCATCTAACAACAATAAAAATACTAATTATAAAAAATTTTCA

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 62.70% 27.00% 4.53% 5.82% NA
All Indica  2759 45.60% 37.50% 7.18% 9.71% NA
All Japonica  1512 91.40% 8.10% 0.33% 0.13% NA
Aus  269 60.60% 36.80% 2.23% 0.37% NA
Indica I  595 74.80% 3.00% 5.04% 17.14% NA
Indica II  465 26.00% 70.50% 0.00% 3.44% NA
Indica III  913 35.30% 42.30% 15.01% 7.45% NA
Indica Intermediate  786 46.90% 38.70% 3.94% 10.43% NA
Temperate Japonica  767 98.80% 0.90% 0.00% 0.26% NA
Tropical Japonica  504 79.20% 20.40% 0.40% 0.00% NA
Japonica Intermediate  241 93.40% 5.40% 1.24% 0.00% NA
VI/Aromatic  96 92.70% 5.20% 1.04% 1.04% NA
Intermediate  90 80.00% 12.20% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217949602 T -> C LOC_Os12g30000-LOC_Os12g30020 intergenic_region ; MODIFIER silent_mutation Average:85.911; most accessible tissue: Minghui63 panicle, score: 98.268 N N N N
vg1217949602 T -> DEL N N silent_mutation Average:85.911; most accessible tissue: Minghui63 panicle, score: 98.268 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)
vg1217949602 T C -0.05 -0.03 -0.04 -0.03 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217949602 8.04E-06 NA mr1023 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
vg1217949602 1.37E-06 NA mr1079 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