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Detailed information for vg1200246210:

Variant ID: vg1200246210 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 246210
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CTGTTCAGATCCATTGCTAAGACATTTTAAAACCACCTTACTGTTGAAGTTAGTGCTACTGGAAGTCTGGAACTGTGGAATATACTAAAATATAGGCATC[G/A]
TGTGAGGTGGTTGTGAGCCTTGTGCGTCATGACCTGTGCAAAGCAAAGTACTATGTGTACTACTAGTATACTTTGTGAAGTTAGTGTCGGTGTCAAATAA

Reverse complement sequence

TTATTTGACACCGACACTAACTTCACAAAGTATACTAGTAGTACACATAGTACTTTGCTTTGCACAGGTCATGACGCACAAGGCTCACAACCACCTCACA[C/T]
GATGCCTATATTTTAGTATATTCCACAGTTCCAGACTTCCAGTAGCACTAACTTCAACAGTAAGGTGGTTTTAAAATGTCTTAGCAATGGATCTGAACAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 10.20% 0.53% 0.63% NA
All Indica  2759 98.30% 0.50% 0.18% 1.01% NA
All Japonica  1512 69.00% 29.80% 1.26% 0.00% NA
Aus  269 98.90% 0.40% 0.00% 0.74% NA
Indica I  595 98.30% 1.00% 0.17% 0.50% NA
Indica II  465 98.90% 0.20% 0.43% 0.43% NA
Indica III  913 98.10% 0.30% 0.00% 1.53% NA
Indica Intermediate  786 98.00% 0.60% 0.25% 1.15% NA
Temperate Japonica  767 50.10% 48.00% 1.96% 0.00% NA
Tropical Japonica  504 95.20% 4.40% 0.40% 0.00% NA
Japonica Intermediate  241 74.30% 24.90% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 1.11% 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
vg1200246210 G -> DEL N N silent_mutation Average:68.384; most accessible tissue: Zhenshan97 root, score: 95.751 N N N N
vg1200246210 G -> A LOC_Os12g01390.1 upstream_gene_variant ; 3515.0bp to feature; MODIFIER silent_mutation Average:68.384; most accessible tissue: Zhenshan97 root, score: 95.751 N N N N
vg1200246210 G -> A LOC_Os12g01380.1 intron_variant ; MODIFIER silent_mutation Average:68.384; most accessible tissue: Zhenshan97 root, score: 95.751 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)
vg1200246210 G A 0.01 0.01 0.0 0.0 0.03 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1200246210 NA 4.93E-10 Heading_date All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1200246210 1.01E-08 NA mr1310 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
vg1200246210 3.88E-07 NA mr1926 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