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Detailed information for vg0106186003:

Variant ID: vg0106186003 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 6186003
Reference Allele: GGCCGCCGCCGCCAlternative Allele: GGCCGCCGCC,G,GGCC
Primary Allele: GGCCGCCGCCGCCSecondary Allele: GGCCGCCGCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCACTCGTCGCCCGTGCCGCGGTACTCGAACTTGGGCAGCGCGGCGATGGCGTCCTCGCCGAGGCCCGGCGCCGGCCGCTTCTTGTTGGTGACGTTCCC[GGCCGCCGCCGCC/GGCCGCCGCC,G,GGCC]
GCCGCCGCCGCCGACGCGGCTGCCACCGTGACCCGGTTCACCGCGCGCCGCATGCGGTAGCACCGTATGGCGCAGAGCACGAGCACGATGACGAGCAGCG

Reverse complement sequence

CGCTGCTCGTCATCGTGCTCGTGCTCTGCGCCATACGGTGCTACCGCATGCGGCGCGCGGTGAACCGGGTCACGGTGGCAGCCGCGTCGGCGGCGGCGGC[GGCGGCGGCGGCC/GGCGGCGGCC,C,GGCC]
GGGAACGTCACCAACAAGAAGCGGCCGGCGCCGGGCCTCGGCGAGGACGCCATCGCCGCGCTGCCCAAGTTCGAGTACCGCGGCACGGGCGACGAGTGCG

Allele Frequencies:

Populations Population SizeFrequency of GGCCGCCGCCGCC(primary allele) Frequency of GGCCGCCGCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.40% 35.00% 0.47% 0.00% GGCC: 0.13%; G: 0.04%
All Indica  2759 41.50% 57.90% 0.62% 0.00% NA
All Japonica  1512 98.60% 0.90% 0.20% 0.00% GGCC: 0.20%; G: 0.07%
Aus  269 98.90% 0.70% 0.00% 0.00% GGCC: 0.37%
Indica I  595 9.70% 89.40% 0.84% 0.00% NA
Indica II  465 39.60% 60.00% 0.43% 0.00% NA
Indica III  913 57.40% 42.20% 0.44% 0.00% NA
Indica Intermediate  786 48.20% 51.00% 0.76% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 97.10% 0.40% 0.83% 0.00% GGCC: 1.24%; G: 0.41%
VI/Aromatic  96 89.60% 9.40% 0.00% 0.00% GGCC: 1.04%
Intermediate  90 60.00% 35.60% 2.22% 0.00% GGCC: 1.11%; G: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106186003 GGCCGCCGCCGCC -> G LOC_Os01g11490.1 disruptive_inframe_deletion ; p.Ala102_Ala105del; MODERATE inframe_variant Average:82.179; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0106186003 GGCCGCCGCCGCC -> GGCCGCCGCC LOC_Os01g11490.1 inframe_deletion ; p.Ala102del; MODERATE inframe_variant Average:82.179; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0106186003 GGCCGCCGCCGCC -> GGCC LOC_Os01g11490.1 inframe_deletion ; p.Ala102_Ala104del; MODERATE inframe_variant Average:82.179; most accessible tissue: Zhenshan97 panicle, score: 89.389 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)
vg0106186003 GGCCG* G 0.01 0.03 0.12 0.0 0.07 0.23
vg0106186003 GGCCG* GGCC 0.05 -0.12 -0.15 0.02 0.04 0.09
vg0106186003 GGCCG* GGCCG* 0.18 0.04 -0.03 0.0 0.07 0.06