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Detailed information for vg0306112685:

Variant ID: vg0306112685 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6112685
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


ATATCATTACTACATTTTTCTTATACAGAATGGCTATATATAATTAATATAAATATTAATTAAACTTAAAAAAGAAAATCTCATAGTATCCCGATACTAC[G/A]
ATACGATCCTACGATACGATATTACTTTGAGCAGAACTATGCTAGTATCGTGATCCTAGCAACCTTGGCAGCTGCGCGAGCAGATGGCCGCGCCGCGGCG

Reverse complement sequence

CGCCGCGGCGCGGCCATCTGCTCGCGCAGCTGCCAAGGTTGCTAGGATCACGATACTAGCATAGTTCTGCTCAAAGTAATATCGTATCGTAGGATCGTAT[C/T]
GTAGTATCGGGATACTATGAGATTTTCTTTTTTAAGTTTAATTAATATTTATATTAATTATATATAGCCATTCTGTATAAGAAAAATGTAGTAATGATAT

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 81.30% 9.20% 8.32% 1.12% NA
All Indica  2759 69.00% 15.00% 14.10% 1.92% NA
All Japonica  1512 99.10% 0.80% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 50.10% 3.90% 40.67% 5.38% NA
Indica II  465 40.90% 58.30% 0.43% 0.43% NA
Indica III  913 94.70% 0.10% 4.27% 0.88% NA
Indica Intermediate  786 70.00% 15.10% 13.49% 1.40% NA
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 85.60% 12.20% 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
vg0306112685 G -> A LOC_Os03g11690.1 upstream_gene_variant ; 2653.0bp to feature; MODIFIER silent_mutation Average:71.682; most accessible tissue: Minghui63 panicle, score: 92.8 N N N N
vg0306112685 G -> A LOC_Os03g11690.2 upstream_gene_variant ; 2653.0bp to feature; MODIFIER silent_mutation Average:71.682; most accessible tissue: Minghui63 panicle, score: 92.8 N N N N
vg0306112685 G -> A LOC_Os03g11680-LOC_Os03g11690 intergenic_region ; MODIFIER silent_mutation Average:71.682; most accessible tissue: Minghui63 panicle, score: 92.8 N N N N
vg0306112685 G -> DEL N N silent_mutation Average:71.682; most accessible tissue: Minghui63 panicle, score: 92.8 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)
vg0306112685 G A 0.01 0.01 0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306112685 NA 5.82E-06 mr1011 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
vg0306112685 6.47E-06 6.45E-06 mr1012 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
vg0306112685 1.48E-06 1.48E-06 mr1313 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
vg0306112685 4.98E-06 4.97E-06 mr1664 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
vg0306112685 NA 5.05E-08 mr1929 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
vg0306112685 NA 7.74E-06 mr1197_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
vg0306112685 NA 4.32E-07 mr1346_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
vg0306112685 NA 8.65E-07 mr1349_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
vg0306112685 NA 5.08E-06 mr1360_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
vg0306112685 NA 2.24E-08 mr1428_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
vg0306112685 NA 5.16E-06 mr1654_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
vg0306112685 1.31E-06 1.31E-06 mr1848_2 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
vg0306112685 NA 2.16E-06 mr1893_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