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Detailed information for vg0219427804:

Variant ID: vg0219427804 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19427804
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.89, C: 0.12, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTCCTCATTTACTCAATTGCCATATCATTTTTTATTTTAGGTGGTAGCTTATTTAATACTATGGATATCATACTAGTCATTGGGTTAGGAATGGAGTA[T/C]
ATGACTTTATTCATTAGGTTCATGTTAAAGACGCGGAAAATGTTTCTACTGGTTTGTTGCTGCGTGTGCGTGCACATTTTTTTTTTGGACCAAATGTGCA

Reverse complement sequence

TGCACATTTGGTCCAAAAAAAAAATGTGCACGCACACGCAGCAACAAACCAGTAGAAACATTTTCCGCGTCTTTAACATGAACCTAATGAATAAAGTCAT[A/G]
TACTCCATTCCTAACCCAATGACTAGTATGATATCCATAGTATTAAATAAGCTACCACCTAAAATAAAAAATGATATGGCAATTGAGTAAATGAGGAAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.40% 48.20% 0.21% 0.25% NA
All Indica  2759 76.60% 22.80% 0.18% 0.40% NA
All Japonica  1512 15.20% 84.50% 0.26% 0.07% NA
Aus  269 5.90% 94.10% 0.00% 0.00% NA
Indica I  595 56.30% 43.40% 0.17% 0.17% NA
Indica II  465 78.70% 21.10% 0.00% 0.22% NA
Indica III  913 92.60% 7.00% 0.11% 0.33% NA
Indica Intermediate  786 72.30% 26.60% 0.38% 0.76% NA
Temperate Japonica  767 5.60% 93.90% 0.39% 0.13% NA
Tropical Japonica  504 26.60% 73.40% 0.00% 0.00% NA
Japonica Intermediate  241 22.00% 77.60% 0.41% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 41.10% 57.80% 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
vg0219427804 T -> DEL N N silent_mutation Average:63.252; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0219427804 T -> C LOC_Os02g32700.1 upstream_gene_variant ; 3854.0bp to feature; MODIFIER silent_mutation Average:63.252; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0219427804 T -> C LOC_Os02g32710.1 downstream_gene_variant ; 3124.0bp to feature; MODIFIER silent_mutation Average:63.252; most accessible tissue: Zhenshan97 root, score: 84.639 N N N N
vg0219427804 T -> C LOC_Os02g32700-LOC_Os02g32710 intergenic_region ; MODIFIER silent_mutation Average:63.252; most accessible tissue: Zhenshan97 root, score: 84.639 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)
vg0219427804 T C 0.04 0.0 0.0 0.03 0.08 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219427804 NA 1.10E-06 mr1213 Jap_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
vg0219427804 NA 1.47E-06 mr1224 Jap_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
vg0219427804 NA 1.04E-06 mr1411 Jap_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
vg0219427804 NA 7.56E-06 mr1437 Jap_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
vg0219427804 NA 1.06E-06 mr1522 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
vg0219427804 NA 2.47E-07 mr1885_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