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Detailed information for vg0517176749:

Variant ID: vg0517176749 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 17176749
Reference Allele: TAlternative Allele: A,TCTCTCTCTCTCTCTC
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGATGGAGGAAATCAAGAAAGGTTGGTGTCGGTGATGACTTATGAGTTGAGAAGACGCGAGGTTTTGCTTCCACTCGTACGGCCGTTTTTGTTTTCTTC[T/A,TCTCTCTCTCTCTCTC]
TCTCTCCAGCTTGTTCTTTAATTTGTTGTTACCTACCCTAGCTGCTTATATTGTGTGTGATTATATTGTGTGTCCTCATCTGTGTGTGTATATGATTGGA

Reverse complement sequence

TCCAATCATATACACACACAGATGAGGACACACAATATAATCACACACAATATAAGCAGCTAGGGTAGGTAACAACAAATTAAAGAACAAGCTGGAGAGA[A/T,GAGAGAGAGAGAGAGA]
GAAGAAAACAAAAACGGCCGTACGAGTGGAAGCAAAACCTCGCGTCTTCTCAACTCATAAGTCATCACCGACACCAACCTTTCTTGATTTCCTCCATCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.30% 2.90% 2.60% 0.00% TCTCTCTCTCTCTCTC: 0.19%
All Indica  2759 92.40% 3.50% 3.95% 0.00% TCTCTCTCTCTCTCTC: 0.14%
All Japonica  1512 97.00% 2.40% 0.53% 0.00% TCTCTCTCTCTCTCTC: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.70% 0.00% 10.25% 0.00% NA
Indica II  465 76.60% 18.50% 4.95% 0.00% NA
Indica III  913 99.60% 0.00% 0.11% 0.00% TCTCTCTCTCTCTCTC: 0.33%
Indica Intermediate  786 95.40% 1.40% 3.05% 0.00% TCTCTCTCTCTCTCTC: 0.13%
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 94.00% 4.80% 1.19% 0.00% NA
Japonica Intermediate  241 96.30% 2.90% 0.41% 0.00% TCTCTCTCTCTCTCTC: 0.41%
VI/Aromatic  96 95.80% 0.00% 0.00% 0.00% TCTCTCTCTCTCTCTC: 4.17%
Intermediate  90 87.80% 5.60% 6.67% 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
vg0517176749 T -> A LOC_Os05g29710.1 3_prime_UTR_variant ; 232.0bp to feature; MODIFIER silent_mutation Average:82.214; most accessible tissue: Callus, score: 92.459 N N N N
vg0517176749 T -> A LOC_Os05g29700.1 upstream_gene_variant ; 4496.0bp to feature; MODIFIER silent_mutation Average:82.214; most accessible tissue: Callus, score: 92.459 N N N N
vg0517176749 T -> TCTCTCTCTCTCTCTC LOC_Os05g29710.1 3_prime_UTR_variant ; 233.0bp to feature; MODIFIER silent_mutation Average:82.214; most accessible tissue: Callus, score: 92.459 N N N N
vg0517176749 T -> TCTCTCTCTCTCTCTC LOC_Os05g29700.1 upstream_gene_variant ; 4497.0bp to feature; MODIFIER silent_mutation Average:82.214; most accessible tissue: Callus, score: 92.459 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)
vg0517176749 T A -0.15 -0.02 -0.01 -0.02 -0.03 -0.01
vg0517176749 T TCTCT* 0.63 0.31 0.12 0.14 0.24 0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517176749 NA 6.05E-08 mr1039 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
vg0517176749 NA 4.72E-06 mr1077 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
vg0517176749 2.77E-06 3.56E-09 mr1415 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
vg0517176749 8.68E-06 8.67E-06 mr1562 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
vg0517176749 NA 2.62E-06 mr1564 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
vg0517176749 2.77E-06 3.56E-09 mr1567 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
vg0517176749 NA 4.88E-07 mr1726 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
vg0517176749 NA 7.29E-08 mr1039_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