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Detailed information for vg0519889030:

Variant ID: vg0519889030 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19889030
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAAGTTTAAAAAAATTGGAACGATGTGATGAAAAGTTTAAAGTTTATGCGTGTAGAAAAATTCGATGTGACGGAAAAATTAGAAGTTTGAAGAAAAAAA[T/A]
TAAAATGTAAACAGGGCCCAACGCAATTCCGGGTTTATTCTCTCCCTCCGTCTCCGTTCAGGTTTATTCTCTCCATCCGCCTCCGTTCACATCAAGCTAT

Reverse complement sequence

ATAGCTTGATGTGAACGGAGGCGGATGGAGAGAATAAACCTGAACGGAGACGGAGGGAGAGAATAAACCCGGAATTGCGTTGGGCCCTGTTTACATTTTA[A/T]
TTTTTTTCTTCAAACTTCTAATTTTTCCGTCACATCGAATTTTTCTACACGCATAAACTTTAAACTTTTCATCACATCGTTCCAATTTTTTTAAACTTTT

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 60.30% 35.00% 4.42% 0.28% NA
All Indica  2759 97.00% 1.40% 1.56% 0.04% NA
All Japonica  1512 2.90% 96.80% 0.26% 0.00% NA
Aus  269 28.60% 8.60% 58.36% 4.46% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 97.80% 1.70% 0.43% 0.00% NA
Indica III  913 96.30% 1.90% 1.75% 0.11% NA
Indica Intermediate  786 95.70% 1.10% 3.18% 0.00% NA
Temperate Japonica  767 3.80% 96.10% 0.13% 0.00% NA
Tropical Japonica  504 2.00% 97.80% 0.20% 0.00% NA
Japonica Intermediate  241 2.10% 97.10% 0.83% 0.00% NA
VI/Aromatic  96 0.00% 96.90% 3.12% 0.00% NA
Intermediate  90 57.80% 40.00% 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
vg0519889030 T -> DEL N N silent_mutation Average:82.129; most accessible tissue: Minghui63 root, score: 96.53 N N N N
vg0519889030 T -> A LOC_Os05g33750-LOC_Os05g33760 intergenic_region ; MODIFIER silent_mutation Average:82.129; most accessible tissue: Minghui63 root, score: 96.53 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)
vg0519889030 T A 0.01 -0.01 0.0 -0.02 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519889030 NA 2.39E-13 mr1013 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
vg0519889030 NA 7.96E-08 mr1045 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
vg0519889030 NA 1.63E-48 mr1125 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
vg0519889030 2.65E-07 2.65E-07 mr1255 Jap_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
vg0519889030 NA 5.05E-13 mr1270 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
vg0519889030 NA 3.40E-10 mr1316 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
vg0519889030 NA 6.55E-21 mr1422 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
vg0519889030 NA 3.83E-08 mr1446 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
vg0519889030 NA 6.52E-12 mr1540 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
vg0519889030 6.08E-06 5.80E-09 mr1691 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
vg0519889030 NA 7.71E-08 mr1716 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
vg0519889030 NA 4.15E-11 mr1720 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
vg0519889030 NA 2.60E-07 mr1785 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
vg0519889030 NA 9.15E-14 mr1807 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
vg0519889030 NA 5.45E-06 mr1955 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
vg0519889030 NA 4.19E-51 mr1121_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
vg0519889030 NA 1.12E-37 mr1208_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
vg0519889030 NA 7.77E-27 mr1270_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
vg0519889030 NA 8.59E-17 mr1720_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