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Detailed information for vg0229208015:

Variant ID: vg0229208015 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 29208015
Reference Allele: GAlternative Allele: GCGCCGC,GCGCCGCCGC
Primary Allele: GSecondary Allele: GCGCCGC

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTTGGGAGGCAGGAGGGGCCTCGAGAAAGCGGCGGAGTCCATCAACGACGACGGCGAGGAAGCCGACGAGCCAAGAACCTGCGGGTGCAGCTGCTGCT[G/GCGCCGC,GCGCCGCCGC]
CGCCGCCGCCGTCGTGTACTGATGGTGACCTTGCTCCTCCTCGTCTTCCTCCTCGTCGTCCTCCTCTTCTTCCTCCTCTTCCTCCTCCTCCACATGCGAT

Reverse complement sequence

ATCGCATGTGGAGGAGGAGGAAGAGGAGGAAGAAGAGGAGGACGACGAGGAGGAAGACGAGGAGGAGCAAGGTCACCATCAGTACACGACGGCGGCGGCG[C/GCGGCGC,GCGGCGGCGC]
AGCAGCAGCTGCACCCGCAGGTTCTTGGCTCGTCGGCTTCCTCGCCGTCGTCGTTGATGGACTCCGCCGCTTTCTCGAGGCCCCTCCTGCCTCCCAACCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GCGCCGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.90% 15.00% 0.02% 0.00% GCGCCGCCGC: 0.04%
All Indica  2759 74.50% 25.50% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.40% 10.40% 0.17% 0.00% NA
Indica II  465 63.00% 37.00% 0.00% 0.00% NA
Indica III  913 72.40% 27.60% 0.00% 0.00% NA
Indica Intermediate  786 72.40% 27.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 0.00% 0.00% GCGCCGCCGC: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0229208015 G -> GCGCCGCCGC LOC_Os02g47770.1 inframe_insertion ; p.Ala39_Gln40insAlaAlaAla; MODERATE inframe_variant Average:90.996; most accessible tissue: Zhenshan97 panicle, score: 96.668 N N N N
vg0229208015 G -> GCGCCGC LOC_Os02g47770.1 inframe_insertion ; p.Ala38_Ala39dup; MODERATE inframe_variant Average:90.996; most accessible tissue: Zhenshan97 panicle, score: 96.668 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)
vg0229208015 G GCGCC* 0.27 0.24 0.28 0.11 0.19 0.3