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Detailed information for vg0916390219:

Variant ID: vg0916390219 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 16390219
Reference Allele: CTGAlternative Allele: C
Primary Allele: CTGSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAAGTTCCCGCTTGAGGCTGTCGTCGAGCCCAAGCTGCCCGCTCACCTCTATGCTGCTGCCTGATGTGATATGCCTTTGATGATGTGCGTGTGTACGTT[CTG/C]
TGTCTCTTGACTGTACTGTAGGCACTGCTCCTGTCGCGGTCCAACATTAAGCTTGCAGTGTATTGCTAGCGTTGTTACTTATTATGCATCCTGTGCTGCC

Reverse complement sequence

GGCAGCACAGGATGCATAATAAGTAACAACGCTAGCAATACACTGCAAGCTTAATGTTGGACCGCGACAGGAGCAGTGCCTACAGTACAGTCAAGAGACA[CAG/G]
AACGTACACACGCACATCATCAAAGGCATATCACATCAGGCAGCAGCATAGAGGTGAGCGGGCAGCTTGGGCTCGACGACAGCCTCAAGCGGGAACTTGC

Allele Frequencies:

Populations Population SizeFrequency of CTG(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.40% 27.40% 0.11% 0.13% NA
All Indica  2759 53.50% 46.10% 0.18% 0.22% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.30% 3.50% 0.00% 0.17% NA
Indica II  465 24.90% 74.40% 0.22% 0.43% NA
Indica III  913 36.40% 63.40% 0.00% 0.22% NA
Indica Intermediate  786 57.90% 41.50% 0.51% 0.13% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 0.00% 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
vg0916390219 CTG -> DEL N N silent_mutation Average:91.788; most accessible tissue: Zhenshan97 young leaf, score: 97.927 N N N N
vg0916390219 CTG -> C LOC_Os09g26960.1 3_prime_UTR_variant ; 40.0bp to feature; MODIFIER silent_mutation Average:91.788; most accessible tissue: Zhenshan97 young leaf, score: 97.927 N N N N
vg0916390219 CTG -> C LOC_Os09g26970.1 upstream_gene_variant ; 2650.0bp to feature; MODIFIER silent_mutation Average:91.788; most accessible tissue: Zhenshan97 young leaf, score: 97.927 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)
vg0916390219 CTG C 0.11 0.07 0.12 0.09 0.12 0.18