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Detailed information for vg0222934216:

Variant ID: vg0222934216 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 22934216
Reference Allele: AAlternative Allele: AGCCACC
Primary Allele: ASecondary Allele: AGCCACC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTTTTTTTTTTTCCGTCGCTTCTTCGCGCCGCCTCCCCTCGACGCCGGCGCCGCCGCTCTCGTGAGCCACCGCCACCGCCGGCGCCGCCGCTCTCGTG[A/AGCCACC]
GCCACCGCCACCGCCGGCGCCGCCGAGCCTCCTCCTCCGGCAAGACGTCTCATCCAGGCCTCTCCCTCCCCCTCAGACGCCGCCTCTGCGCCTCCATTCT

Reverse complement sequence

AGAATGGAGGCGCAGAGGCGGCGTCTGAGGGGGAGGGAGAGGCCTGGATGAGACGTCTTGCCGGAGGAGGAGGCTCGGCGGCGCCGGCGGTGGCGGTGGC[T/GGTGGCT]
CACGAGAGCGGCGGCGCCGGCGGTGGCGGTGGCTCACGAGAGCGGCGGCGCCGGCGTCGAGGGGAGGCGGCGCGAAGAAGCGACGGAAAAAAAAAAAAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AGCCACC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 2.40% 1.69% 0.00% NA
All Indica  2759 97.60% 1.70% 0.72% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 53.90% 24.90% 21.19% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.50% 0.90% 0.65% 0.00% NA
Indica III  913 96.20% 3.10% 0.77% 0.00% NA
Indica Intermediate  786 96.90% 1.80% 1.27% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg0222934216 A -> AGCCACC LOC_Os02g37950.1 5_prime_UTR_variant ; 1325.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 N N N N
vg0222934216 A -> AGCCACC LOC_Os02g37950.2 5_prime_UTR_variant ; 1325.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 N N N N
vg0222934216 A -> AGCCACC LOC_Os02g37950.3 5_prime_UTR_variant ; 1325.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 N N N N
vg0222934216 A -> AGCCACC LOC_Os02g37940.1 upstream_gene_variant ; 723.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 N N N N
vg0222934216 A -> AGCCACC LOC_Os02g37940.2 upstream_gene_variant ; 672.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 N N N N
vg0222934216 A -> AGCCACC LOC_Os02g37930.1 downstream_gene_variant ; 3739.0bp to feature; MODIFIER silent_mutation Average:98.825; most accessible tissue: Zhenshan97 flower, score: 99.535 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)
vg0222934216 A AGCCA* -0.18 -0.13 -0.05 -0.17 -0.11 -0.12