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Detailed information for vg0225007778:

Variant ID: vg0225007778 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25007778
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTGCCACCGTGCAGCGCCTTGCCGCGGGAGACGTCGATGAGCGGGTTGTCGTTCACGGAGTTGATCTCACGCTCGATGGACTTGGTGGCGGCGCGGAT[A/G]
ACCTCAATTTGAGGGCCGAGCCACTGTGGGGATGTCCGGAGCGCGTACCGGTCTTGCTTCGGCTTCATCAGTGGGTCGAGCTCACCAAGCTTCTTGGCAT

Reverse complement sequence

ATGCCAAGAAGCTTGGTGAGCTCGACCCACTGATGAAGCCGAAGCAAGACCGGTACGCGCTCCGGACATCCCCACAGTGGCTCGGCCCTCAAATTGAGGT[T/C]
ATCCGCGCCGCCACCAAGTCCATCGAGCGTGAGATCAACTCCGTGAACGACAACCCGCTCATCGACGTCTCCCGCGGCAAGGCGCTGCACGGTGGCAACT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 77.10% 0.30% 0.87% 21.69% NA
All Indica  2759 62.90% 0.50% 1.30% 35.27% NA
All Japonica  1512 98.50% 0.10% 0.26% 1.19% NA
Aus  269 92.90% 0.00% 0.37% 6.69% NA
Indica I  595 46.40% 0.50% 1.51% 51.60% NA
Indica II  465 74.00% 0.00% 1.94% 24.09% NA
Indica III  913 56.20% 1.00% 0.99% 41.84% NA
Indica Intermediate  786 76.60% 0.40% 1.15% 21.88% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 95.40% 0.20% 0.79% 3.57% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 2.08% NA
Intermediate  90 84.40% 0.00% 0.00% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225007778 A -> G LOC_Os02g41680.1 synonymous_variant ; p.Val363Val; LOW synonymous_codon Average:82.846; most accessible tissue: Zhenshan97 root, score: 94.124 N N N N
vg0225007778 A -> DEL LOC_Os02g41680.1 N frameshift_variant Average:82.846; most accessible tissue: Zhenshan97 root, score: 94.124 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)
vg0225007778 A G 0.0 0.0 0.0 0.0 0.0 0.01