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Detailed information for vg0414057794:

Variant ID: vg0414057794 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 14057794
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, T: 0.26, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


AGTGCAAGGGTAACCATCGGACATGGCAACTTTGATGTATACTTGCTCGATGCCTACAGTTCGAAGAGGATAATCTTGTGTTCGCTTACCCAGCCTACCA[A/T]
TATTGATGACACCAGTGACGAGGGTGAGTGCCAACGGAATATTCCCATCGTCCGTGGTTTTCAACTCCAGTTTGTCCATCGGCATGAACACGGCGAAGGC

Reverse complement sequence

GCCTTCGCCGTGTTCATGCCGATGGACAAACTGGAGTTGAAAACCACGGACGATGGGAATATTCCGTTGGCACTCACCCTCGTCACTGGTGTCATCAATA[T/A]
TGGTAGGCTGGGTAAGCGAACACAAGATTATCCTCTTCGAACTGTAGGCATCGAGCAAGTATACATCAAAGTTGCCATGTCCGATGGTTACCCTTGCACT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.40% 28.30% 6.31% 1.02% NA
All Indica  2759 58.00% 37.90% 3.26% 0.80% NA
All Japonica  1512 88.10% 0.40% 10.19% 1.32% NA
Aus  269 3.30% 95.50% 1.12% 0.00% NA
Indica I  595 51.60% 37.10% 8.91% 2.35% NA
Indica II  465 86.70% 12.50% 0.86% 0.00% NA
Indica III  913 51.60% 47.50% 0.88% 0.00% NA
Indica Intermediate  786 53.40% 42.40% 3.18% 1.02% NA
Temperate Japonica  767 97.50% 0.00% 2.22% 0.26% NA
Tropical Japonica  504 83.90% 1.20% 13.10% 1.79% NA
Japonica Intermediate  241 66.80% 0.00% 29.46% 3.73% NA
VI/Aromatic  96 44.80% 10.40% 41.67% 3.12% NA
Intermediate  90 63.30% 21.10% 12.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0414057794 A -> DEL LOC_Os04g24510.1 N frameshift_variant Average:83.231; most accessible tissue: Zhenshan97 young leaf, score: 90.815 N N N N
vg0414057794 A -> T LOC_Os04g24510.1 missense_variant ; p.Asn169Ile; MODERATE nonsynonymous_codon Average:83.231; most accessible tissue: Zhenshan97 young leaf, score: 90.815 unknown unknown TOLERATED 0.15

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)
vg0414057794 A T 0.08 0.06 0.03 0.01 0.06 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0414057794 NA 2.12E-07 mr1006 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
vg0414057794 NA 5.26E-06 mr1007 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
vg0414057794 NA 5.69E-07 mr1037 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
vg0414057794 NA 5.66E-07 mr1052 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
vg0414057794 NA 6.32E-10 mr1066 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
vg0414057794 NA 6.20E-08 mr1066 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
vg0414057794 NA 2.88E-06 mr1073 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
vg0414057794 NA 4.26E-06 mr1209 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
vg0414057794 NA 1.69E-06 mr1216 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
vg0414057794 NA 3.69E-09 mr1275 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
vg0414057794 NA 8.53E-07 mr1392 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
vg0414057794 NA 9.11E-06 mr1397 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
vg0414057794 NA 2.07E-06 mr1665 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
vg0414057794 4.91E-07 NA mr1705 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
vg0414057794 2.23E-06 3.62E-07 mr1705 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
vg0414057794 NA 2.19E-10 mr1730 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
vg0414057794 NA 4.95E-07 mr1764 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
vg0414057794 NA 5.03E-06 mr1835 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
vg0414057794 NA 1.33E-06 mr1887 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
vg0414057794 NA 1.78E-06 mr1977_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