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Detailed information for vg0135122922:

Variant ID: vg0135122922 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 35122922
Reference Allele: TGAGAlternative Allele: TGAGGAG,T
Primary Allele: TGAGSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACTGTACCGATCGATCGATTGATGGAGTGAGCTAGCCAAGTACCTTCTGTGATCTCTTTCCCACACGATCGAGCTGGATTAGTATTTCGGGAGATGAGA[TGAG/TGAGGAG,T]
GAGGAGGAGGAGAATCAACAACAGCAAGTGGAGTTGAGCCGTAGTAGTAGTAGCAGTAGACAGCGATCCGTCGCGAGATGCCACGAGAGATTTATAATGG

Reverse complement sequence

CCATTATAAATCTCTCGTGGCATCTCGCGACGGATCGCTGTCTACTGCTACTACTACTACGGCTCAACTCCACTTGCTGTTGTTGATTCTCCTCCTCCTC[CTCA/CTCCTCA,A]
TCTCATCTCCCGAAATACTAATCCAGCTCGATCGTGTGGGAAAGAGATCACAGAAGGTACTTGGCTAGCTCACTCCATCAATCGATCGATCGGTACAGTT

Allele Frequencies:

Populations Population SizeFrequency of TGAG(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.00% 0.00% TGAGGAG: 0.04%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 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  786 100.00% 0.00% 0.00% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 0.00% 0.00% TGAGGAG: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0135122922 TGAG -> T LOC_Os01g60730.1 5_prime_UTR_variant ; 308.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 N N N N
vg0135122922 TGAG -> T LOC_Os01g60730.2 5_prime_UTR_variant ; 308.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 N N N N
vg0135122922 TGAG -> T LOC_Os01g60720.1 upstream_gene_variant ; 2923.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 N N N N
vg0135122922 TGAG -> TGAGGAG LOC_Os01g60730.1 5_prime_UTR_variant ; 311.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 N N N N
vg0135122922 TGAG -> TGAGGAG LOC_Os01g60730.2 5_prime_UTR_variant ; 311.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 N N N N
vg0135122922 TGAG -> TGAGGAG LOC_Os01g60720.1 upstream_gene_variant ; 2926.0bp to feature; MODIFIER silent_mutation Average:99.297; most accessible tissue: Minghui63 flower, score: 99.809 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)
vg0135122922 TGAG T 0.06 0.01 -0.01 -0.08 0.01 0.06
vg0135122922 TGAG TGAGG* 0.12 0.03 0.08 0.0 0.0 0.0