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Detailed information for vg0217962243:

Variant ID: vg0217962243 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 17962243
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


TATTGAACTACCACTGATGCTTCCCCACCATTCAAGAAATTTGAACCCATGTGTTATAATCGTTGATTTTTTTAAAAAAAATAGGTCAAATATGAAATAT[G/C]
ATAAAAAAAAGAGTAGTTTCATTGATTTCTAAGTGGTTGTTCAGATTGTAGCTAAAATAAACTTTACAAAATTTTGGCAATATTGCCAAATTGCTAAAAT

Reverse complement sequence

ATTTTAGCAATTTGGCAATATTGCCAAAATTTTGTAAAGTTTATTTTAGCTACAATCTGAACAACCACTTAGAAATCAATGAAACTACTCTTTTTTTTAT[C/G]
ATATTTCATATTTGACCTATTTTTTTTAAAAAAATCAACGATTATAACACATGGGTTCAAATTTCTTGAATGGTGGGGAAGCATCAGTGGTAGTTCAATA

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 53.70% 23.70% 0.63% 21.96% NA
All Indica  2759 26.70% 37.30% 0.87% 35.12% NA
All Japonica  1512 97.30% 0.40% 0.07% 2.25% NA
Aus  269 66.20% 28.30% 0.00% 5.58% NA
Indica I  595 29.40% 18.00% 0.67% 51.93% NA
Indica II  465 40.00% 11.40% 0.22% 48.39% NA
Indica III  913 19.90% 70.00% 0.66% 9.42% NA
Indica Intermediate  786 24.60% 29.40% 1.65% 44.40% NA
Temperate Japonica  767 98.70% 0.00% 0.00% 1.30% NA
Tropical Japonica  504 95.80% 0.80% 0.00% 3.37% NA
Japonica Intermediate  241 95.90% 0.80% 0.41% 2.90% NA
VI/Aromatic  96 94.80% 0.00% 1.04% 4.17% NA
Intermediate  90 67.80% 10.00% 4.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0217962243 G -> DEL N N silent_mutation Average:70.559; most accessible tissue: Zhenshan97 root, score: 92.253 N N N N
vg0217962243 G -> C LOC_Os02g30210.1 upstream_gene_variant ; 520.0bp to feature; MODIFIER silent_mutation Average:70.559; most accessible tissue: Zhenshan97 root, score: 92.253 N N N N
vg0217962243 G -> C LOC_Os02g30210.2 upstream_gene_variant ; 1273.0bp to feature; MODIFIER silent_mutation Average:70.559; most accessible tissue: Zhenshan97 root, score: 92.253 N N N N
vg0217962243 G -> C LOC_Os02g30210-LOC_Os02g30219 intergenic_region ; MODIFIER silent_mutation Average:70.559; most accessible tissue: Zhenshan97 root, score: 92.253 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)
vg0217962243 G C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0217962243 NA 2.12E-06 mr1138 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
vg0217962243 3.72E-06 1.10E-06 mr1169 Ind_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
vg0217962243 2.13E-06 NA mr1855 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
vg0217962243 NA 3.71E-06 mr1806_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
vg0217962243 2.07E-08 NA mr1855_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
vg0217962243 9.43E-07 NA mr1855_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