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Detailed information for vg0228809054:

Variant ID: vg0228809054 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 28809054
Reference Allele: CTGAlternative Allele: C,GTG
Primary Allele: CTGSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCTCGCGCGCCACTCTCCCGCCCAGGCGCCTCTCTCTCTCTCTCTAGTTTCTCGCACCACCTGCCTACATATCGCCACAGCCGCTGTCGTCGTCTCGTCT[CTG/C,GTG]
TGTGTGTGTCTCCATCAGACGCCGGCCATATAGCTAGCGAGACCGGCACATTCCCATCGGGAATCCGCCTCGGGCTTCGCCGCAATCCCACGCTAACTCA

Reverse complement sequence

TGAGTTAGCGTGGGATTGCGGCGAAGCCCGAGGCGGATTCCCGATGGGAATGTGCCGGTCTCGCTAGCTATATGGCCGGCGTCTGATGGAGACACACACA[CAG/G,CAC]
AGACGAGACGACGACAGCGGCTGTGGCGATATGTAGGCAGGTGGTGCGAGAAACTAGAGAGAGAGAGAGAGGCGCCTGGGCGGGAGAGTGGCGCGCGAGG

Allele Frequencies:

Populations Population SizeFrequency of CTG(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 2.60% 0.00% 0.00% GTG: 0.04%
All Indica  2759 99.30% 0.60% 0.00% 0.00% GTG: 0.07%
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 61.30% 38.70% 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 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.30% 0.00% 0.00% GTG: 0.25%
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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0228809054 CTG -> C LOC_Os02g47190.1 5_prime_UTR_variant ; 286.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> C LOC_Os02g47180.1 downstream_gene_variant ; 3063.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> C LOC_Os02g47200.1 downstream_gene_variant ; 3336.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> C LOC_Os02g47180.2 downstream_gene_variant ; 3063.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> GTG LOC_Os02g47190.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> GTG LOC_Os02g47190.1 5_prime_UTR_variant ; 297.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> GTG LOC_Os02g47180.1 downstream_gene_variant ; 3062.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> GTG LOC_Os02g47200.1 downstream_gene_variant ; 3337.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 N N N N
vg0228809054 CTG -> GTG LOC_Os02g47180.2 downstream_gene_variant ; 3062.0bp to feature; MODIFIER silent_mutation Average:97.008; most accessible tissue: Minghui63 flag leaf, score: 99.576 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)
vg0228809054 CTG C -0.33 -0.02 0.0 -0.09 -0.1 -0.12
vg0228809054 CTG GTG -0.01 -0.04 0.0 -0.02 -0.01 0.03