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Detailed information for vg0823069336:

Variant ID: vg0823069336 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 23069336
Reference Allele: TAlternative Allele: TGTGAAAA,TACTGCC,TTGAGAAC
Primary Allele: TSecondary Allele: TACTGCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGGTCCGGAGCCACTGGTGCTCGCTGTAGATAAGAAACGGTTCCCACCGATGGGATAATAGTTTTGAATGATAAAAAGTTGCTTCAATAATATTTTGC[T/TGTGAAAA,TACTGCC,TTGAGAAC]
CAGCGACCAGGGACACTCGCTGACCGTCGGCATCGTGCAGCCGCGCAAGCTCATCGTGGACACCGGCAGCGACCTCATCTGGACGCAGTGCAAGCTGTCC

Reverse complement sequence

GGACAGCTTGCACTGCGTCCAGATGAGGTCGCTGCCGGTGTCCACGATGAGCTTGCGCGGCTGCACGATGCCGACGGTCAGCGAGTGTCCCTGGTCGCTG[A/TTTTCACA,GGCAGTA,GTTCTCAA]
GCAAAATATTATTGAAGCAACTTTTTATCATTCAAAACTATTATCCCATCGGTGGGAACCGTTTCTTATCTACAGCGAGCACCAGTGGCTCCGGACCTGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TACTGCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.20% 0.06% 0.00% TTGAGAAC: 0.08%; TGTGAAAA: 0.02%
All Indica  2759 99.60% 0.20% 0.11% 0.00% TTGAGAAC: 0.11%; TGTGAAAA: 0.04%
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.40% 0.00% 0.00% TTGAGAAC: 0.37%
Indica I  595 99.80% 0.00% 0.00% 0.00% TGTGAAAA: 0.17%
Indica II  465 98.70% 0.90% 0.43% 0.00% NA
Indica III  913 99.70% 0.00% 0.00% 0.00% TTGAGAAC: 0.33%
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0823069336 T -> TTGAGAAC LOC_Os08g36540.1 frameshift_variant ; p.Ser12fs; HIGH N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TTGAGAAC LOC_Os08g36530.1 downstream_gene_variant ; 2357.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TTGAGAAC LOC_Os08g36550.1 downstream_gene_variant ; 2826.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TACTGCC LOC_Os08g36540.1 disruptive_inframe_insertion ; p.Leu11_Ser12insLeuPro; MODERATE N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TACTGCC LOC_Os08g36530.1 downstream_gene_variant ; 2357.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TACTGCC LOC_Os08g36550.1 downstream_gene_variant ; 2826.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TGTGAAAA LOC_Os08g36540.1 frameshift_variant&stop_gained ; p.Ser12fs; HIGH N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TGTGAAAA LOC_Os08g36530.1 downstream_gene_variant ; 2357.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 N N N N
vg0823069336 T -> TGTGAAAA LOC_Os08g36550.1 downstream_gene_variant ; 2826.0bp to feature; MODIFIER N Average:81.681; most accessible tissue: Minghui63 root, score: 93.056 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)
vg0823069336 T TACTG* 0.06 0.05 0.05 0.07 0.03 -0.08
vg0823069336 T TGTGA* -0.23 -0.12 -0.04 0.04 -0.04 -0.11
vg0823069336 T TTGAG* -0.18 -0.14 -0.08 -0.01 -0.08 -0.15