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Detailed information for vg0728679906:

Variant ID: vg0728679906 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 28679906
Reference Allele: CGAGTTGCCATGCAAAGGCATAlternative Allele: TGAGTTGCCATGCAAAGGCAT,C
Primary Allele: CGAGTTGCCATGCAAAGGCA TSecondary Allele: TGAGTTGCCATGCAAAGGCA T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTGTGGCCATCTCATCACTTTCATGGTTCAATGGTTTCATCAGCAAGTGCACGGAACAGACTAGAGAGTGTAGGTGTATGCATGTGTGATGTCATGTAA[CGAGTTGCCATGCAAAGGCAT/TGAGTTGCCATGCAAAGGCAT,C]
GAGGATTACGGACCTCTCTTTCGTCGTAATCCTAGCAGCTACAGATTTCAACTGTCGTGTTAACCAAGTGAAGTGCTAGTTTCGAATGTATTGGCCCCTC

Reverse complement sequence

GAGGGGCCAATACATTCGAAACTAGCACTTCACTTGGTTAACACGACAGTTGAAATCTGTAGCTGCTAGGATTACGACGAAAGAGAGGTCCGTAATCCTC[ATGCCTTTGCATGGCAACTCG/ATGCCTTTGCATGGCAACTCA,G]
TTACATGACATCACACATGCATACACCTACACTCTCTAGTCTGTTCCGTGCACTTGCTGATGAAACCATTGAACCATGAAAGTGATGAGATGGCCACAGC

Allele Frequencies:

Populations Population SizeFrequency of CGAGTTGCCATGCAAAGGCA T(primary allele) Frequency of TGAGTTGCCATGCAAAGGCA T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 1.00% 0.28% 0.00% C: 0.02%
All Indica  2759 99.70% 0.20% 0.11% 0.00% C: 0.04%
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 79.90% 16.40% 3.72% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.00% C: 0.11%
Indica Intermediate  786 99.20% 0.60% 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  96 100.00% 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
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> TGAGTTGCCATGCAAAGGCAT LOC_Os07g48030.1 3_prime_UTR_variant ; 176.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> TGAGTTGCCATGCAAAGGCAT LOC_Os07g48040.1 upstream_gene_variant ; 4212.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> TGAGTTGCCATGCAAAGGCAT LOC_Os07g48020.1 downstream_gene_variant ; 4473.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> C LOC_Os07g48030.1 3_prime_UTR_variant ; 180.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> C LOC_Os07g48040.1 upstream_gene_variant ; 4211.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 N N N N
vg0728679906 CGAGTTGCCATGCAAAGGCAT -> C LOC_Os07g48020.1 downstream_gene_variant ; 4474.0bp to feature; MODIFIER silent_mutation Average:83.196; most accessible tissue: Zhenshan97 panicle, score: 89.389 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)
vg0728679906 CGAGT* C -0.13 0.03 -0.02 -0.23 -0.35 -0.4
vg0728679906 CGAGT* TGAGT* -0.01 -0.02 -0.02 -0.02 -0.03 -0.02