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Detailed information for vg1018666697:

Variant ID: vg1018666697 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 18666697
Reference Allele: TGCCGCCAlternative Allele: TGCCGCCGCC,T
Primary Allele: TGCCGCCSecondary Allele: TGCCGCCGCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATCGACACGATAGTGACGGAGCACCGCAAGCTCTTCCTTGCGGTGCTCATGCTTTCCCTTCTTAGGTGTCGCGTACGCCTTCTTCTTTCGCTTCTTGT[TGCCGCC/TGCCGCCGCC,T]
GCCGCCACCACAGATGCGACCGAGGAGGTGCAGCGTCGACTCCTCCTGAATACCATAGTAGATTAGCGTGTGGCCGTCGTCCAGCTGATGCCCCTGGAAG

Reverse complement sequence

CTTCCAGGGGCATCAGCTGGACGACGGCCACACGCTAATCTACTATGGTATTCAGGAGGAGTCGACGCTGCACCTCCTCGGTCGCATCTGTGGTGGCGGC[GGCGGCA/GGCGGCGGCA,A]
ACAAGAAGCGAAAGAAGAAGGCGTACGCGACACCTAAGAAGGGAAAGCATGAGCACCGCAAGGAAGAGCTTGCGGTGCTCCGTCACTATCGTGTCGATGA

Allele Frequencies:

Populations Population SizeFrequency of TGCCGCC(primary allele) Frequency of TGCCGCCGCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.40% 0.60% 0.02% 0.00% T: 0.02%
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 97.80% 0.00% 1.11% 0.00% T: 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
vg1018666697 TGCCGCC -> T LOC_Os10g34990.1 inframe_deletion ; p.Gly83_Gly84del; MODERATE N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> T LOC_Os10g34970.1 upstream_gene_variant ; 3527.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> T LOC_Os10g35000.1 upstream_gene_variant ; 477.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> T LOC_Os10g34980.1 downstream_gene_variant ; 1869.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> T LOC_Os10g35010.1 downstream_gene_variant ; 3279.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> TGCCGCCGCC LOC_Os10g34990.1 inframe_insertion ; p.Gly82dup; MODERATE N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> TGCCGCCGCC LOC_Os10g34970.1 upstream_gene_variant ; 3533.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> TGCCGCCGCC LOC_Os10g35000.1 upstream_gene_variant ; 471.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> TGCCGCCGCC LOC_Os10g34980.1 downstream_gene_variant ; 1875.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 N N N N
vg1018666697 TGCCGCC -> TGCCGCCGCC LOC_Os10g35010.1 downstream_gene_variant ; 3273.0bp to feature; MODIFIER N Average:93.363; most accessible tissue: Callus, score: 98.185 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)
vg1018666697 TGCCG* T -0.01 -0.15 -0.12 -0.06 -0.04 -0.05
vg1018666697 TGCCG* TGCCG* 0.36 0.39 0.39 0.22 0.36 0.4