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Detailed information for vg1217900467:

Variant ID: vg1217900467 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17900467
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, C: 0.22, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TAACAATGTTTTACACATCTCTGACCTTTTGTACCATTTATACTATACAGTTTTTTTAAAAAAAACTACTCATATTATATTGCATGTACACACAAAATTA[G/C]
AGCGCCATTGTTTTGCTTACCCGATAGCTTATTAGCAAATAAAAGATCATTTATGAGTAAAACTTTTATATACATGTCCTTAACGACTTAAAACCAAATA

Reverse complement sequence

TATTTGGTTTTAAGTCGTTAAGGACATGTATATAAAAGTTTTACTCATAAATGATCTTTTATTTGCTAATAAGCTATCGGGTAAGCAAAACAATGGCGCT[C/G]
TAATTTTGTGTGTACATGCAATATAATATGAGTAGTTTTTTTTAAAAAAACTGTATAGTATAAATGGTACAAAAGGTCAGAGATGTGTAAAACATTGTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.50% 27.00% 8.25% 8.19% NA
All Indica  2759 38.20% 37.50% 10.62% 13.70% NA
All Japonica  1512 89.70% 4.00% 6.08% 0.20% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 50.40% 47.90% 0.67% 1.01% NA
Indica II  465 27.10% 25.80% 25.81% 21.29% NA
Indica III  913 34.40% 38.80% 9.75% 17.09% NA
Indica Intermediate  786 39.90% 35.00% 10.18% 14.89% NA
Temperate Japonica  767 99.10% 0.40% 0.26% 0.26% NA
Tropical Japonica  504 75.20% 8.50% 16.27% 0.00% NA
Japonica Intermediate  241 90.00% 6.20% 3.32% 0.41% NA
VI/Aromatic  96 34.40% 60.40% 3.12% 2.08% NA
Intermediate  90 65.60% 27.80% 2.22% 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
vg1217900467 G -> C LOC_Os12g29950.1 upstream_gene_variant ; 463.0bp to feature; MODIFIER silent_mutation Average:51.662; most accessible tissue: Callus, score: 94.582 N N N N
vg1217900467 G -> C LOC_Os12g29950.2 upstream_gene_variant ; 463.0bp to feature; MODIFIER silent_mutation Average:51.662; most accessible tissue: Callus, score: 94.582 N N N N
vg1217900467 G -> C LOC_Os12g29940-LOC_Os12g29950 intergenic_region ; MODIFIER silent_mutation Average:51.662; most accessible tissue: Callus, score: 94.582 N N N N
vg1217900467 G -> DEL N N silent_mutation Average:51.662; most accessible tissue: Callus, score: 94.582 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)
vg1217900467 G C 0.0 0.0 0.0 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217900467 NA 1.84E-06 mr1115 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
vg1217900467 NA 6.87E-06 mr1364 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
vg1217900467 NA 2.12E-07 mr1627 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
vg1217900467 3.20E-06 NA mr1775 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
vg1217900467 2.52E-06 NA mr1788 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
vg1217900467 NA 1.54E-06 mr1115_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
vg1217900467 NA 1.46E-06 mr1498_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
vg1217900467 NA 9.42E-07 mr1583_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
vg1217900467 NA 8.71E-06 mr1611_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