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Detailed information for vg0626719833:

Variant ID: vg0626719833 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 26719833
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, A: 0.08, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


ATACCATGCCAGAACCACTCACCTCTGACGATCCACCATTACTCGTCACGGATTGAAGTTATAAGATCAATAATCTTTAACAGGATCAAACCGGTTAAGA[C/A]
CTTGTTCGATTAATCCCTATGTGGAAGAGATTGGATGGAATTTATTCCACAGTTATTATAGTGTGGAATTATTCTGCCTCAATCTCTTCCAATCCTGTTC

Reverse complement sequence

GAACAGGATTGGAAGAGATTGAGGCAGAATAATTCCACACTATAATAACTGTGGAATAAATTCCATCCAATCTCTTCCACATAGGGATTAATCGAACAAG[G/T]
TCTTAACCGGTTTGATCCTGTTAAAGATTATTGATCTTATAACTTCAATCCGTGACGAGTAATGGTGGATCGTCAGAGGTGAGTGGTTCTGGCATGGTAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.90% 39.80% 0.15% 0.15% NA
All Indica  2759 41.50% 58.10% 0.18% 0.25% NA
All Japonica  1512 96.60% 3.20% 0.13% 0.00% NA
Aus  269 25.70% 74.30% 0.00% 0.00% NA
Indica I  595 29.20% 69.90% 0.17% 0.67% NA
Indica II  465 21.70% 78.10% 0.00% 0.22% NA
Indica III  913 52.80% 46.90% 0.22% 0.11% NA
Indica Intermediate  786 49.20% 50.40% 0.25% 0.13% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 92.50% 7.10% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 0.00% 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
vg0626719833 C -> A LOC_Os06g44280.1 downstream_gene_variant ; 2263.0bp to feature; MODIFIER silent_mutation Average:78.355; most accessible tissue: Zhenshan97 panicle, score: 92.784 N N N N
vg0626719833 C -> A LOC_Os06g44280-LOC_Os06g44290 intergenic_region ; MODIFIER silent_mutation Average:78.355; most accessible tissue: Zhenshan97 panicle, score: 92.784 N N N N
vg0626719833 C -> DEL N N silent_mutation Average:78.355; most accessible tissue: Zhenshan97 panicle, score: 92.784 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)
vg0626719833 C A -0.01 -0.02 -0.01 -0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0626719833 1.16E-06 NA mr1064 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
vg0626719833 1.79E-08 1.94E-09 mr1064 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
vg0626719833 2.48E-06 NA mr1534 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
vg0626719833 2.40E-07 6.93E-08 mr1534 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
vg0626719833 NA 1.78E-06 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