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Detailed information for vg0323734872:

Variant ID: vg0323734872 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 23734872
Reference Allele: CAGTAAGTGTGTTTAGCTTTAAAAACGAlternative Allele: C
Primary Allele: CAGTAAGTGTGTTTAGCTTT AAAAACGSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCTTCGCCACCCGCGCCATCGCCGACGTCGACCTCAACAAGTGCGAGCCATGGGACCTCCCCAGTAAGTCTCTAGCTAACTCTTCGATTTCGATCCC[CAGTAAGTGTGTTTAGCTTTAAAAACG/C]
AGTTTTGAAGGGAGAAATTGTGAGCATATTGAGGATTGAACACGGAACATTCGCGGGTTGAAATTGAAGTGCATCTCTAAATTGTGTTTAGCTTTGATTC

Reverse complement sequence

GAATCAAAGCTAAACACAATTTAGAGATGCACTTCAATTTCAACCCGCGAATGTTCCGTGTTCAATCCTCAATATGCTCACAATTTCTCCCTTCAAAACT[CGTTTTTAAAGCTAAACACACTTACTG/G]
GGGATCGAAATCGAAGAGTTAGCTAGAGACTTACTGGGGAGGTCCCATGGCTCGCACTTGTTGAGGTCGACGTCGGCGATGGCGCGGGTGGCGAAGCCGA

Allele Frequencies:

Populations Population SizeFrequency of CAGTAAGTGTGTTTAGCTTT AAAAACG(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.20% 32.40% 0.40% 0.00% NA
All Indica  2759 47.00% 52.30% 0.69% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 78.10% 21.90% 0.00% 0.00% NA
Indica I  595 74.30% 24.40% 1.34% 0.00% NA
Indica II  465 14.00% 85.80% 0.22% 0.00% NA
Indica III  913 46.90% 52.80% 0.33% 0.00% NA
Indica Intermediate  786 46.20% 52.90% 0.89% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0323734872 CAGTAAGTGTGTTTAGCTTTAAAAACG -> C LOC_Os03g42650.1 upstream_gene_variant ; 4012.0bp to feature; MODIFIER silent_mutation Average:76.607; most accessible tissue: Zhenshan97 root, score: 90.081 N N N N
vg0323734872 CAGTAAGTGTGTTTAGCTTTAAAAACG -> C LOC_Os03g42650.2 upstream_gene_variant ; 4012.0bp to feature; MODIFIER silent_mutation Average:76.607; most accessible tissue: Zhenshan97 root, score: 90.081 N N N N
vg0323734872 CAGTAAGTGTGTTTAGCTTTAAAAACG -> C LOC_Os03g42630.1 intron_variant ; MODIFIER silent_mutation Average:76.607; most accessible tissue: Zhenshan97 root, score: 90.081 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)
vg0323734872 CAGTA* C -0.39 -0.74 -0.98 -0.38 -0.38 -0.13