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Detailed information for vg0103097517:

Variant ID: vg0103097517 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3097517
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAATAATGGTAATGATATGACGAGCAATAATTCAACCAAAAATGGACAGAACATTAAGAAAAGAACACCTTTTCAACAACAAAAAAAATTAAGAGAGA[A/G]
AAAAAACAACAGAAAAAATTATGGAAGGCGCGTACAATACAGAGATCTCGCTCAAACTTGTCATCAACCTCATCGTCACAGCCCCAACCAGACGCTCGCC

Reverse complement sequence

GGCGAGCGTCTGGTTGGGGCTGTGACGATGAGGTTGATGACAAGTTTGAGCGAGATCTCTGTATTGTACGCGCCTTCCATAATTTTTTCTGTTGTTTTTT[T/C]
TCTCTCTTAATTTTTTTTGTTGTTGAAAAGGTGTTCTTTTCTTAATGTTCTGTCCATTTTTGGTTGAATTATTGCTCGTCATATCATTACCATTATTATT

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 92.30% 0.10% 4.99% 2.60% NA
All Indica  2759 99.20% 0.00% 0.40% 0.40% NA
All Japonica  1512 77.80% 0.30% 14.68% 7.21% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 0.00% 1.18% 0.17% NA
Indica II  465 99.10% 0.00% 0.22% 0.65% NA
Indica III  913 99.50% 0.00% 0.11% 0.44% NA
Indica Intermediate  786 99.40% 0.00% 0.25% 0.38% NA
Temperate Japonica  767 94.80% 0.00% 4.82% 0.39% NA
Tropical Japonica  504 49.80% 1.00% 31.75% 17.46% NA
Japonica Intermediate  241 82.20% 0.00% 10.37% 7.47% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 0.00% 3.33% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103097517 A -> G LOC_Os01g06580.1 3_prime_UTR_variant ; 76.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06560.1 upstream_gene_variant ; 4652.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06560.2 upstream_gene_variant ; 4652.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06570.1 downstream_gene_variant ; 1587.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06590.1 downstream_gene_variant ; 1911.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06590.2 downstream_gene_variant ; 1911.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> G LOC_Os01g06590.3 downstream_gene_variant ; 2129.0bp to feature; MODIFIER silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 N N N N
vg0103097517 A -> DEL N N silent_mutation Average:85.995; most accessible tissue: Zhenshan97 flag leaf, score: 96.785 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)
vg0103097517 A G 0.02 -0.02 -0.03 -0.03 -0.03 -0.03