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Detailed information for vg0823069333:

Variant ID: vg0823069333 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 23069333
Reference Allele: TGCAlternative Allele: TTGTGAAAACACTTGAGAACCAAGCATCACTAGC,T,TTGTGAAAACACTTGAGAACCAAGC,TTGTGAAAACACTTGAGC,TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC,TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTCCTGATTCATTGTACTAGC
Primary Allele: TGCSecondary Allele: TTGTGAAAACACTTGAGAAC CAAGCATCACTAGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGGCAGGTCCGGAGCCACTGGTGCTCGCTGTAGATAAGAAACGGTTCCCACCGATGGGATAATAGTTTTGAATGATAAAAAGTTGCTTCAATAATATTT[TGC/TTGTGAAAACACTTGAGAACCAAGCATCACTAGC,T,TTGTGAAAACACTTGAGAACCAAGC,TTGTGAAAACACTTGAGC,TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC,TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCGTGTCCTGATTCATTGTACTAGC]
TCAGCGACCAGGGACACTCGCTGACCGTCGGCATCGTGCAGCCGCGCAAGCTCATCGTGGACACCGGCAGCGACCTCATCTGGACGCAGTGCAAGCTGTC

Reverse complement sequence

GACAGCTTGCACTGCGTCCAGATGAGGTCGCTGCCGGTGTCCACGATGAGCTTGCGCGGCTGCACGATGCCGACGGTCAGCGAGTGTCCCTGGTCGCTGA[GCA/GCTAGTGATGCTTGGTTCTCAAGTGTTTTCACAA,A,GCTTGGTTCTCAAGTGTTTTCACAA,GCTCAAGTGTTTTCACAA,GCTAGTACAATGAATCAGGACATGGGCAGTAGCTAGTGATGCTTGGTTCTCAAGTGTTTTCACAA,GCTAGTACAATGAATCAGGACACGGGCAGTAGCTAGTGATGCTTGGTTCTCAAGTGTTTTCACAA]
AAATATTATTGAAGCAACTTTTTATCATTCAAAACTATTATCCCATCGGTGGGAACCGTTTCTTATCTACAGCGAGCACCAGTGGCTCCGGACCTGCCGT

Allele Frequencies:

Populations Population SizeFrequency of TGC(primary allele) Frequency of TTGTGAAAACACTTGAGAAC CAAGCATCACTAGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.40% 1.00% 11.07% 7.62% TTGTGAAAACACTTGAGAACCAAGC: 0.63%; TTGTGAAAACACTTGAGC: 0.17%; TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC: 0.08%; T: 0.02%
All Indica  2759 66.00% 1.40% 18.19% 12.90% TTGTGAAAACACTTGAGAACCAAGC: 0.98%; TTGTGAAAACACTTGAGC: 0.29%; TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC: 0.14%; T: 0.04%
All Japonica  1512 99.70% 0.00% 0.20% 0.07% NA
Aus  269 92.90% 1.50% 4.46% 0.00% TTGTGAAAACACTTGAGAACCAAGC: 1.12%
Indica I  595 51.80% 0.70% 36.30% 9.58% TTGTGAAAACACTTGAGAACCAAGC: 1.34%; T: 0.17%; TTGTGAAAACACTTGAGC: 0.17%
Indica II  465 60.20% 2.80% 18.06% 17.20% TTGTGAAAACACTTGAGAACCAAGC: 1.29%; TTGTGAAAACACTTGAGC: 0.22%; TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC: 0.22%
Indica III  913 78.40% 1.20% 6.24% 12.49% TTGTGAAAACACTTGAGAACCAAGC: 1.10%; TTGTGAAAACACTTGAGC: 0.33%; TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC: 0.22%
Indica Intermediate  786 65.90% 1.40% 18.45% 13.36% TTGTGAAAACACTTGAGC: 0.38%; TTGTGAAAACACTTGAGAACCAAGC: 0.38%; TTGTGAAAACACTTGAGAACCAAGCATCACTAGCTACTGCCCATGTCCTGATTCATTGTACTAGC: 0.13%
Temperate Japonica  767 99.50% 0.00% 0.39% 0.13% 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 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 87.80% 2.20% 6.67% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGCATCAC TAGCTACTGCCCATGTCCTGATTCATTGTA CTAGC LOC_Os08g36540.1 frameshift_variant ; p.Leu10fs; HIGH frameshift_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGC LOC_Os08g36540.1 disruptive_inframe_insertion ; p.Leu10delinsPheValLysThrLeuGl u; MODERATE inframe_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGC LOC_Os08g36540.1 frameshift_variant ; p.Leu10fs; HIGH frameshift_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> T LOC_Os08g36540.1 frameshift_variant ; p.Leu10fs; HIGH frameshift_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> DEL LOC_Os08g36540.1 N frameshift_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGCATCAC TAGC LOC_Os08g36540.1 frameshift_variant ; p.Leu10fs; HIGH frameshift_variant Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGCATCAC TAGCTACTGCCCGTGTCCTGATTCATTGTA CTAGC LOC_Os08g36540.1 frameshift_variant ; p.Leu10fs; HIGH N Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGCATCAC TAGCTACTGCCCGTGTCCTGATTCATTGTA CTAGC LOC_Os08g36530.1 downstream_gene_variant ; 2354.0bp to feature; MODIFIER N Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 N N N N
vg0823069333 TGC -> TTGTGAAAACACTTGAGAACCAAGCATCAC TAGCTACTGCCCGTGTCCTGATTCATTGTA CTAGC LOC_Os08g36550.1 downstream_gene_variant ; 2829.0bp to feature; MODIFIER N Average:81.928; most accessible tissue: Minghui63 root, score: 93.342 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)
vg0823069333 TGC T 0.03 0.03 0.07 -0.01 0.01 0.02
vg0823069333 TGC TTGTG* -0.36 -0.09 0.03 -0.14 -0.2 -0.23