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Detailed information for vg0918209461:

Variant ID: vg0918209461 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 18209461
Reference Allele: GAlternative Allele: GCACCAC,GCAC,GCACCACCACCACCACCAC,GCACCACCAC
Primary Allele: GSecondary Allele: GCACCAC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCCACTGACATGTGGGCCAGTGGGCATTTTCTCTGCTGCCTTAGACAAAAGCTAAAGGCGAGCACTTTGTCATTGTGTGTACTCCTCCACTGTGCAGG[G/GCACCAC,GCAC,GCACCACCACCACCACCAC,GCACCACCAC]
CACCACCACCACCACCACCAGTGGACGCTCCCCTTCGCCGGCGTCGGGCAGGTGGCCGCCACCGCGGCGAGGCAGCAGCAGGAGTGGAAGGGGCGAGTCG

Reverse complement sequence

CGACTCGCCCCTTCCACTCCTGCTGCTGCCTCGCCGCGGTGGCGGCCACCTGCCCGACGCCGGCGAAGGGGAGCGTCCACTGGTGGTGGTGGTGGTGGTG[C/GTGGTGC,GTGC,GTGGTGGTGGTGGTGGTGC,GTGGTGGTGC]
CCTGCACAGTGGAGGAGTACACACAATGACAAAGTGCTCGCCTTTAGCTTTTGTCTAAGGCAGCAGAGAAAATGCCCACTGGCCCACATGTCAGTGGGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GCACCAC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 45.50% 41.10% 0.30% 0.00% GCAC: 13.06%; GCACCACCAC: 0.02%; GCACCACCACCACCACCAC: 0.02%
All Indica  2759 19.50% 70.00% 0.47% 0.00% GCAC: 10.04%; GCACCACCAC: 0.04%; GCACCACCACCACCACCAC: 0.04%
All Japonica  1512 99.60% 0.00% 0.00% 0.00% GCAC: 0.40%
Aus  269 9.70% 0.00% 0.00% 0.00% GCAC: 90.33%
Indica I  595 48.70% 40.50% 0.84% 0.00% GCAC: 9.92%
Indica II  465 10.80% 81.70% 0.00% 0.00% GCAC: 7.53%
Indica III  913 2.50% 89.50% 0.33% 0.00% GCAC: 7.56%; GCACCACCAC: 0.11%
Indica Intermediate  786 22.10% 62.60% 0.64% 0.00% GCAC: 14.50%; GCACCACCACCACCACCAC: 0.13%
Temperate Japonica  767 99.90% 0.00% 0.00% 0.00% GCAC: 0.13%
Tropical Japonica  504 99.40% 0.00% 0.00% 0.00% GCAC: 0.60%
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.00% GCAC: 0.83%
VI/Aromatic  96 22.90% 0.00% 0.00% 0.00% GCAC: 77.08%
Intermediate  90 64.40% 15.60% 1.11% 0.00% GCAC: 18.89%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0918209461 G -> GCACCACCACCACCACCAC LOC_Os09g29930.1 disruptive_inframe_insertion ; p.His126_His131dup; MODERATE inframe_variant Average:99.862; most accessible tissue: Zhenshan97 panicle, score: 99.958 N N N N
vg0918209461 G -> GCACCAC LOC_Os09g29930.1 disruptive_inframe_insertion ; p.His130_His131dup; MODERATE inframe_variant Average:99.862; most accessible tissue: Zhenshan97 panicle, score: 99.958 N N N N
vg0918209461 G -> GCACCACCAC LOC_Os09g29930.1 disruptive_inframe_insertion ; p.His129_His131dup; MODERATE inframe_variant Average:99.862; most accessible tissue: Zhenshan97 panicle, score: 99.958 N N N N
vg0918209461 G -> GCAC LOC_Os09g29930.1 disruptive_inframe_insertion ; p.His131dup; MODERATE inframe_variant Average:99.862; most accessible tissue: Zhenshan97 panicle, score: 99.958 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)
vg0918209461 G GCAC 0.04 0.03 0.01 0.06 0.03 0.05
vg0918209461 G GCACC* 0.08 0.08 0.01 0.16 0.04 0.05