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Detailed information for vg1217897242:

Variant ID: vg1217897242 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17897242
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTCGACGAAGGTCAGTGCCGTGCCCACGTTATGTCTCTCGGGGTCATAGGACCCAAGTAAATTATTACTACCTCTACCCCTAAATATTTAATACC[G/A]
TTGACTTTTTTAATATGTTTGACCGTTCGTCTTATTTCAAAACTTTTATAAAATATATAAAACTATATGTATATGTAAAAGTATATTTAACAATGAATCA

Reverse complement sequence

TGATTCATTGTTAAATATACTTTTACATATACATATAGTTTTATATATTTTATAAAAGTTTTGAAATAAGACGAACGGTCAAACATATTAAAAAAGTCAA[C/T]
GGTATTAAATATTTAGGGGTAGAGGTAGTAATAATTTACTTGGGTCCTATGACCCCGAGAGACATAACGTGGGCACGGCACTGACCTTCGTCGAAAAAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.80% 5.50% 4.13% 0.53% NA
All Indica  2759 89.70% 2.90% 6.49% 0.83% NA
All Japonica  1512 95.20% 4.60% 0.07% 0.13% NA
Aus  269 71.40% 23.80% 4.83% 0.00% NA
Indica I  595 70.40% 7.20% 19.50% 2.86% NA
Indica II  465 97.00% 0.20% 2.58% 0.22% NA
Indica III  913 97.00% 1.10% 1.75% 0.11% NA
Indica Intermediate  786 91.60% 3.40% 4.45% 0.51% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 92.90% 6.70% 0.20% 0.20% NA
Japonica Intermediate  241 87.60% 12.00% 0.00% 0.41% NA
VI/Aromatic  96 60.40% 39.60% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg1217897242 G -> DEL N N silent_mutation Average:74.274; most accessible tissue: Minghui63 root, score: 92.748 N N N N
vg1217897242 G -> A LOC_Os12g29950.1 upstream_gene_variant ; 3688.0bp to feature; MODIFIER silent_mutation Average:74.274; most accessible tissue: Minghui63 root, score: 92.748 N N N N
vg1217897242 G -> A LOC_Os12g29950.2 upstream_gene_variant ; 3688.0bp to feature; MODIFIER silent_mutation Average:74.274; most accessible tissue: Minghui63 root, score: 92.748 N N N N
vg1217897242 G -> A LOC_Os12g29940.1 downstream_gene_variant ; 2685.0bp to feature; MODIFIER silent_mutation Average:74.274; most accessible tissue: Minghui63 root, score: 92.748 N N N N
vg1217897242 G -> A LOC_Os12g29940-LOC_Os12g29950 intergenic_region ; MODIFIER silent_mutation Average:74.274; most accessible tissue: Minghui63 root, score: 92.748 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)
vg1217897242 G A -0.07 -0.02 -0.04 -0.07 -0.06 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217897242 4.55E-06 NA mr1858 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
vg1217897242 4.72E-06 NA mr1859 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