## 2 Results
### Transcriptome Results
#### 2.4.2 Differential Expression of Genes of C18 and P1 Colonies  
The differential expression of genes (DEGs) between samples was identified via \(\mid\) log\({}^{2}\) (foldchange) \(\mid\)\(\geq\) 1 & P adj \(\leq\) 0.05. The Venn diagram (Figure 6a) exhibited that there are 620 independent DEGs in the WT. Additionally, there are 443 and 281 independent DEGs in C18 and P1, respectively. These three groups shared 11,034 DEGs. C18 and P1 shared 782 DEGs, which is more than those shared by C18 and WT (584 DEGs), and P1 and the WT (289 DEGs).  
\begin{table}
\begin{tabular}{c c c c c c c c c c} \hline \hline
**Sample** & \begin{tabular}{c} **Raw** \\ **Reads 1** \\ \end{tabular} & \begin{tabular}{c} **Raw** \\ **Bases 2** \\ \end{tabular} & \begin{tabular}{c} **Clean** \\ **Reads 3** \\ \end{tabular} & \begin{tabular}{c} **Clean** \\ **Bases 4** \\ \end{tabular} & \begin{tabular}{c} **Error** \\ **Rate 5** \\ \end{tabular} & \begin{tabular}{c} **Q30 (\%) 6** \\ \end{tabular} & \
\begin{tabular}{c} **GC Pet 7** \\ **Map Pet 8** \\ \end{tabular} &
\begin{tabular}{c} **Total** \\ **Map 9** \\ \end{tabular} \\ \hline WT-1 & 45,897,466 & 6.88 G & 43,481,436 & 6.52 G & 0.03 & 90.57 & 62.75 & 95.04\% & 92.66\% \\ WT-2 & 45,372,590 & 6.81 G & 43,300,230 & 6.5 G & 0.03 & 90.04 & 62.97 & 95.08\% & 92.72\% \\ WT-3 & 47,243,698 & 7.09 G & 45,441,558 & 6.82 G & 0.03 & 90.75 & 62.68 & 94.98\% & 92.53\% \\ C18-1 & 45,981,798 & 6.9 G & 43,321,074 & 6.5 G & 0.03 & 90.29 & 61.28 & 87.64\% & 83.55\% \\ C18-2 & 47,989,038 & 7.2 G & 45,152,476 & 6.77 G & 0.03 & 90.53 & 62.04 & 90.40\% & 87.63\% \\ C18-3 & 49,309,270 & 7.4 G & 46,452,078 & 6.97 G & 0.03 & 89.37 & 63.72 & 93.53\% & 90.35\% \\ P1-1 & 51,821,018 & 7.77 G & 48,753,422 & 7.31 G & 0.03 & 92.94 & 61.93 & 87.88\% & 84.91\% \\ P1-2 & 48,975,588 & 7.35 G & 46,310,808 & 6.95 G & 0.03 & 93.22 & 62.65 & 89.23\% & 86.45\% \\ P1-3 & 42,490,208 & 6.37 G & 39,192,990 & 5.88 G & 0.03 & 91.93 & 61.33 & 82.86\% & 80.43\% \\ \hline \hline \end{tabular}  
* Raw reads: number of reads in raw data; 2 raw bases: number of bases of the raw data (raw base = raw reads \(\times\) 150 bp); 3 clean reads: number of reads after raw data filtering; 4 clean bases: raw data filtered bases (clean base = clean reads \(\times\) 150 bp); 5 error rate: data overall sequencing error rate; 6 Q30 (%): percentage of total bases with phred values greater than 30,7 GC pet: percentage of G and C bases in the four bases in clean reads; 8 Total map: percentage of clean reads aligned to the genome; 9 percentage of clean reads aligned to unique positions of the reference genome (for subsequent quantitative data analysis of reads).  
\begin{tabular}{c c c c c c c c} \hline \hline \multicolumn{6}{c}{Pearson correlation between samples} \\ \hline P1\_3 & 0.70\% & 0.711 & 0.71\% & 0.83\% & 0.82\% & 0.83\% & 0.82\% & 0.82\% \\ P1\_2 & 0.74\% & 0.67\% & 0.68\% & 0.81\% & 0.70\% & 0.82\% & 0.83\% & 0.82\% \\ P1\_3 & 0.70\% & 0.712 & 0.70\% & 0.82\% & 0.82\Briefly, 3994 up-regulated and 3140 down-regulated genes were identified in C18 vs. WT (Figure 6b). Likewise, transcriptome data indicated that 3702 up-regulated and 4583 down-regulated genes were identified in P1 vs. WT (Figure 6c). This revealed significant differences between DEGs from C18 versus those from P1 relative to those from the WT, while P1 vs. C18 also had 1711 up-regulated genes vs. 3732 down-regulated genes, indicating that there are also a large number of differences in gene expression levels between these two \(BKT\) gene-overexpressing strains.