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Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios ... Figure 1. Optimization of the variant.

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Presentation on theme: "Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios ... Figure 1. Optimization of the variant."— Presentation transcript:

1 Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios ... Figure 1. Optimization of the variant calling algorithm, ADIScan1, by tangential conversion of read depth ratios between the reference allele and an alternative allele. (A) Three-dimensional chart showing 35,000 variants (mostly at the top) and non-variants (mostly at the bottom). Three axes show the information on read depth for reference and alternative alleles, and Adiscore 1 to distinguish true variants as 1 and non-variant as 0. (B) Fitting process to a general model f(x,y) = 1/(1 + exp (–(a*(tan(min (1, y/x) – 0.5) + c))) to calculate three constants a, b, and c. (C) Three-dimensional chart showing heterozygotic variants (top) and homozygotic variants (bottom). (D) Fitting process to a general model f(x,y) = 1 / (1 + exp (–(a*(tan (min(1, y/x) – 0.5) + c))) to determine three constants a, b and c. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 46, Issue 15, 05 June 2018, Page e92, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 3. Comparison of single-nucleotide variant (SNV) concordance called by four different algorithms. (A) Female ... Figure 3. Comparison of single-nucleotide variant (SNV) concordance called by four different algorithms. (A) Female twins. B. Male twins. Numbers in the Venn diagrams at the far left side indicate variants in non-repetitive regions of the genome called by ADIScan2, GATK, MuTect and VarScan based on the BAM files generated by BME-GATK alignment. Following diagrams show SNVs in non-repetitive regions, repetitive-regions, and both regions combined, in order. Three numbers separated by slashes are PCR-failure cases and correct variants, followed by incorrect variants. Concordant SNVs among the four methods were identified by matching genomic coordinates and custom Venn diagrams drawn in the website Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 46, Issue 15, 05 June 2018, Page e92, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 2. Process of Differential score generation
Figure 2. Process of Differential score generation. X- and Y-axes show bin numbers assigned by the ratios of two ... Figure 2. Process of Differential score generation. X- and Y-axes show bin numbers assigned by the ratios of two allelic sequence reads. An extreme, homozygote (Homo), has all reads with only one allelic sequence, and an assigned bin number of 1. The alternative extreme, heterozygote (Het), has an equal number of the two alleles and an assigned bin number of 21. Paired allelic fractions are in the same direction and homo/homo represents identical sequences in both testers (A–C). (A) Ratio of bin numbers in two testers. (B) Inverse tangential conversion of the bin-number ratios. Value of Homo/Het and Het/Homo increased. (C) Differential score calculated by logarithmic conversion of the tangential values with applying predefined weights and subsequent adjustment of the score based on the allelic ratios. (D) Differential score calculated for cases in which each tester has different sequences although both were homozygotes and represented homo/alternative homo (Homo/Homo). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, Volume 46, Issue 15, 05 June 2018, Page e92, The content of this slide may be subject to copyright: please see the slide notes for details.

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