# Reference Mapping Considering Swaps of Adjacent Bases
## 5 Conclusions  
The SOAP3-swap proposed in this paper has the same functionality as that of SOAP3-dp and also improves the alignment ratio by taking biologically significant swaps into account for the first time. The reason why we considered the swaps with lengths of up to three is because swaps with lengths longer than three hardly occur in our experiment. Further research is necessary to develop more efficient alignment methods that can be applied to situations including exchanges involving non-adjacent bases. Y.K. and M.K. are the main developers and analyzed SOAP3-dp and implemented SOAP3-swap. [PERSON]-[PERSON] and [PERSON] analyzed SOAP2 and SOAP3 and designed the parallel technique together. [PERSON] provided biological support and designed the experiments. [PERSON] provided algorithmic and biological support and is the manager in charge of the project. All authors read and approved the final manuscript. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MSIP) (No. 2021R1H1A2011633); by the Genome Program for Fostering New Post-Genome Industry of the National Research Foundation (NRF) funded by the Korean Government (MSIP) (NRF-2014M3C9A3064706); by the Institute of Information & Communications Technology Planning & Evaluation (IITP) grant funded by the Korean Government (MSIT) \begin{table}
\begin{tabular}{c c c c c c} \hline \hline  & \multirow{2}{*}{**Swap Cost**} & \multicolumn{4}{c}{**Swapped Block Size**} \\ \cline{3-6}  & & **1** & **2** & **3** & **Total** \\ \hline \multirow{3}{*}{Human genome} & \(S_{SW}=-1\) & 265,727 & 7631 & 21 & 273,379 \\  & \(S_{SW}=-2\) & 202,850 & 117 & 31 & 202,998 \\  & \(S_{SW}=-3\) & 145,054 & 57 & 6 & 145,117 \\ \hline \multirow{3}{*}{Drosophila genome} & \(S_{SW}=-1\) & 304,209 & 13,919 & 215 & 318,343 \\  & \(S_{SW}=-2\) & 212,278 & 627 & 273 & 213,178 \\ \cline{1-1}  & \(S_{SW}=-3\) & 158,953 & 79 & 72 & 159,104 \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Number of read pairs including at least one swap according to the swap cost and the swapped block size among all the read pairs aligned by SOAP3-swap. (2020-0-01389, Artificial Intelligence Convergence Research Center (Inha University)); and by INHA UNIVERSITY Research Grant. **Institutional Review Board Statement:** Not applicable. **Informed Consent Statement:** Not applicable. **Data Availability Statement:** The software SOAP3-swap is available for download at [[https://github.com/yhkim8505/SOAP3-swap](https://github.com/yhkim8505/SOAP3-swap)]([https://github.com/yhkim8505/SOAP3-swap](https://github.com/yhkim8505/SOAP3-swap)) (accessed on 28 May 2021). **Acknowledgments:** Not applicable. **Conflicts of Interest:** The authors declare no conflict of interest. **Sample Availability:** For the human genome, the reference sequence, GRCh38, is available at: [[http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set_fna.gz](http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set_fna.gz)]([http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set_fna.gz](http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_full_analysis_set_fna.gz)) (accessed on 28 th May 2021). The read sequences and source codes used in the manuscript are available from the corresponding author on reasonable request. For the drosophila genome, the reference sequence, DydRS2, is available at: [[https://www.ncbi.nlm.nih.gov/assembly/GCF_003285905.1/](https://www.ncbi.nlm.nih.gov/assembly/GCF_003285905.1/)]([https://www.ncbi.nlm.nih.gov/assembly/GCF_003285905.1/](https://www.ncbi.nlm.nih.gov/assembly/GCF_003285905.1/)) (accessed on 28 th May 2021).