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Detailed information for vg1113116826:

Variant ID: vg1113116826 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13116826
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTACTCATCCCCTCAAGTCCCGTCTTCCGCCGTCGCCGGAAACGCTCTCCCCACGCTCTCCCTCTCTCTCCACCTCCGGCCGCCGCTCCAGCCGCCAT[T/G]
CGCCGTCGCCCCGGCCGTCGCCGGTCAGCGCCACCACCTCTCCGCAAAGTCGAGCTCTACCCCAGCCACCCGTTCTTTTGCGCCGAACCCCTCCAGAAGT

Reverse complement sequence

ACTTCTGGAGGGGTTCGGCGCAAAAGAACGGGTGGCTGGGGTAGAGCTCGACTTTGCGGAGAGGTGGTGGCGCTGACCGGCGACGGCCGGGGCGACGGCG[A/C]
ATGGCGGCTGGAGCGGCGGCCGGAGGTGGAGAGAGAGGGAGAGCGTGGGGAGAGCGTTTCCGGCGACGGCGGAAGACGGGACTTGAGGGGATGAGTAGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.50% 1.70% 2.96% 7.81% NA
All Indica  2759 79.80% 2.40% 4.82% 12.90% NA
All Japonica  1512 99.70% 0.10% 0.07% 0.20% NA
Aus  269 94.10% 4.10% 1.12% 0.74% NA
Indica I  595 77.30% 1.80% 7.39% 13.45% NA
Indica II  465 82.20% 0.40% 5.16% 12.26% NA
Indica III  913 79.00% 5.00% 3.29% 12.71% NA
Indica Intermediate  786 81.40% 1.00% 4.45% 13.10% NA
Temperate Japonica  767 99.60% 0.10% 0.00% 0.26% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 1.10% 3.33% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1113116826 T -> DEL LOC_Os11g22800.1 N frameshift_variant Average:75.447; most accessible tissue: Minghui63 flag leaf, score: 93.797 N N N N
vg1113116826 T -> G LOC_Os11g22800.1 missense_variant ; p.Glu128Ala; MODERATE nonsynonymous_codon ; E128A Average:75.447; most accessible tissue: Minghui63 flag leaf, score: 93.797 unknown unknown TOLERATED 1.00

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)
vg1113116826 T G 0.01 0.01 0.02 0.01 0.02 0.02