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Detailed information for vg0426640431:

Variant ID: vg0426640431 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 26640431
Reference Allele: TCAlternative Allele: T
Primary Allele: TCSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCCATGAGCGAGTTCCTCGGCATCAACTAGGCGGGAGCGTACGCTCTTTCTTCCGTACAGTTCGTCGCCGAAGTGTAAATTCGTCAGTTTCTTTTTTT[TC/T]
CCCCTCTTTTTCAGAGGTGTAAATCGTGCCGTGCATGTGTAGTAGTTAAACTTACTGGCTTGTAGTGTTGAGTTTGGACTTCGAAGCCATGAGTTGTGCG

Reverse complement sequence

CGCACAACTCATGGCTTCGAAGTCCAAACTCAACACTACAAGCCAGTAAGTTTAACTACTACACATGCACGGCACGATTTACACCTCTGAAAAAGAGGGG[GA/A]
AAAAAAAGAAACTGACGAATTTACACTTCGGCGACGAACTGTACGGAAGAAAGAGCGTACGCTCCCGCCTAGTTGATGCCGAGGAACTCGCTCATGGAGA

Allele Frequencies:

Populations Population SizeFrequency of TC(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.60% 4.40% 0.00% 0.00% NA
All Indica  2759 97.10% 2.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 54.60% 45.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 94.90% 5.10% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0426640431 TC -> T LOC_Os04g45020.1 3_prime_UTR_variant ; 74.0bp to feature; MODIFIER silent_mutation Average:86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0426640431 TC -> T LOC_Os04g45040.1 upstream_gene_variant ; 3590.0bp to feature; MODIFIER silent_mutation Average:86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0426640431 TC -> T LOC_Os04g45040.3 upstream_gene_variant ; 3590.0bp to feature; MODIFIER silent_mutation Average:86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0426640431 TC -> T LOC_Os04g45040.2 upstream_gene_variant ; 3643.0bp to feature; MODIFIER silent_mutation Average:86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 N N N N
vg0426640431 TC -> T LOC_Os04g45030.1 downstream_gene_variant ; 1739.0bp to feature; MODIFIER silent_mutation Average:86.034; most accessible tissue: Zhenshan97 flower, score: 91.994 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)
vg0426640431 TC T -0.07 0.03 0.11 0.03 0.08 0.12