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Detailed information for vg0431151753:

Variant ID: vg0431151753 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 31151753
Reference Allele: TAlternative Allele: C,TC
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGGGTAGTGGCGGCCAGCGGCTCAGCGCTTCGACAGGAATATTCAACTTTAAAATTCTAGCTCCACCACTGGATACACACACCAAAAGAAAACCCAT[T/C,TC]
CGTTACCTCAAAAAGTGGAGGATCTACTCTGCAGTGATCTACTCTGCAGTTCCGAGTCTCCGACTCTGAAGCTATTGCTCCGCGTAAGCGCTAATTCGCG

Reverse complement sequence

CGCGAATTAGCGCTTACGCGGAGCAATAGCTTCAGAGTCGGAGACTCGGAACTGCAGAGTAGATCACTGCAGAGTAGATCCTCCACTTTTTGAGGTAACG[A/G,GA]
ATGGGTTTTCTTTTGGTGTGTGTATCCAGTGGTGGAGCTAGAATTTTAAAGTTGAATATTCCTGTCGAAGCGCTGAGCCGCTGGCCGCCACTACCCCTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.00% 32.60% 0.57% 32.27% TC: 0.63%
All Indica  2759 4.90% 43.10% 0.65% 51.18% TC: 0.14%
All Japonica  1512 79.50% 18.00% 0.13% 2.38% NA
Aus  269 65.40% 14.90% 1.86% 14.50% TC: 3.35%
Indica I  595 3.70% 30.60% 1.01% 64.71% NA
Indica II  465 5.20% 37.40% 0.65% 56.77% NA
Indica III  913 2.50% 56.50% 0.55% 39.98% TC: 0.44%
Indica Intermediate  786 8.40% 40.50% 0.51% 50.64% NA
Temperate Japonica  767 76.80% 22.60% 0.26% 0.39% NA
Tropical Japonica  504 92.70% 2.20% 0.00% 5.16% NA
Japonica Intermediate  241 60.60% 36.50% 0.00% 2.90% NA
VI/Aromatic  96 51.00% 18.80% 0.00% 15.62% TC: 14.58%
Intermediate  90 47.80% 21.10% 2.22% 25.56% TC: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431151753 T -> C LOC_Os04g52420.1 intron_variant ; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 root, score: 94.001 N N N N
vg0431151753 T -> DEL N N silent_mutation Average:64.519; most accessible tissue: Minghui63 root, score: 94.001 N N N N
vg0431151753 T -> TC LOC_Os04g52420.1 intron_variant ; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 root, score: 94.001 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)
vg0431151753 T C -0.1 -0.03 -0.05 -0.03 -0.07 -0.07
vg0431151753 T TC -0.23 0.03 0.02 0.04 0.01 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431151753 NA 5.16E-08 mr1301 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
vg0431151753 NA 4.72E-09 mr1342 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
vg0431151753 NA 5.19E-09 mr1637 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
vg0431151753 NA 5.55E-07 mr1748 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
vg0431151753 NA 2.45E-07 mr1804 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
vg0431151753 NA 1.91E-11 mr1883 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
vg0431151753 2.11E-06 NA mr1805_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
vg0431151753 2.31E-06 NA mr1805_2 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