\documentclass[a4paper,11pt,oneside]{article}
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\begin{document}
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\section*{\large{NanoOK report for ZF-screens\_MARC\_phase\_1a\_e\_coli\_run1}}
\subsection*{Pass and fail counts}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c}
{\bf Type} & {\bf Pass} & {\bf Fail} \\
Template & 0 & 42240  \\
Complement & 0 & 21712  \\
2D & 0 & 10858  \\
\end{tabular}
}
\end{table}
\subsection*{Read lengths}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c c c c c c c}
{\bf Type} & {\bf NumReads} & {\bf TotalBases} & {\bf Mean} & {\bf Longest} & {\bf Shortest} & {\bf N50} & {\bf N50Count} & {\bf N90} & {\bf N90Count} \\
Template & 42240 & 150713664 & 3568.03 & 449250 & 6 & 4999 & 9665 & 2488 & 27194 \\
Complement & 21712 & 77520815 & 3570.41 & 340137 & 11 & 4847 & 5273 & 2349 & 14633 \\
2D & 10858 & 44220237 & 4072.60 & 30921 & 122 & 5033 & 3004 & 2859 & 7912 \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{figure}[H]
\centering
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_Template_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_Complement_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_2D_lengths.png}
\end{figure}
\subsection*{Template alignments}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c}
Number of reads & 42240 & \\
Number of reads with alignments & 19835 & (46.96\%) \\
Number of reads without alignments & 22405 & (53.04\%) \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c c c c c}
          &             & {\bf Number of} & {\bf \% of} & {\bf Mean read} & {\bf Aligned} & {\bf Mean} & {\bf Longest} \\
{\bf ID} & {\bf Size} & {\bf Reads}     & {\bf Reads}  & {\bf length}    & {\bf bases}   & {\bf coverage} & {\bf Perf Kmer} \\
Control sequence & 3560 & 7718 & 18.27 & 2951.98 & 21411529 & 6014.47 & 63 \\
Escherichia coli & 4641652 & 12117 & 28.69 & 5499.03 & 59043707 & 12.72 & 66 \\
\end{tabular}
}
\end{table}
\subsection*{Complement alignments}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c}
Number of reads & 21712 & \\
Number of reads with alignments & 11048 & (50.88\%) \\
Number of reads without alignments & 10664 & (49.12\%) \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c c c c c}
          &             & {\bf Number of} & {\bf \% of} & {\bf Mean read} & {\bf Aligned} & {\bf Mean} & {\bf Longest} \\
{\bf ID} & {\bf Size} & {\bf Reads}     & {\bf Reads}  & {\bf length}    & {\bf bases}   & {\bf coverage} & {\bf Perf Kmer} \\
Control sequence & 3560 & 4053 & 18.67 & 2764.51 & 9247595 & 2597.64 & 52 \\
Escherichia coli & 4641652 & 6995 & 32.22 & 5404.19 & 31670134 & 6.82 & 72 \\
\end{tabular}
}
\end{table}
\subsection*{2D alignments}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c}
Number of reads & 10858 & \\
Number of reads with alignments & 8823 & (81.26\%) \\
Number of reads without alignments & 2035 & (18.74\%) \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c c c c c}
          &             & {\bf Number of} & {\bf \% of} & {\bf Mean read} & {\bf Aligned} & {\bf Mean} & {\bf Longest} \\
{\bf ID} & {\bf Size} & {\bf Reads}     & {\bf Reads}  & {\bf length}    & {\bf bases}   & {\bf coverage} & {\bf Perf Kmer} \\
Control sequence & 3560 & 3620 & 33.34 & 3117.51 & 11344153 & 3186.56 & 167 \\
Escherichia coli & 4641652 & 5203 & 47.92 & 5394.57 & 28221949 & 6.08 & 182 \\
\end{tabular}
}
\end{table}
\clearpage
\subsection*{Control sequence error analysis}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c}
 & Template & Complement & 2D \\
Overall base identity (excluding indels) & 62.58\% & 53.43\% & 75.16\% \\
Aligned base identity (excluding indels) & 79.67\% & 79.66\% & 86.51\% \\
Identical bases per 100 aligned bases (including indels) & 66.59\% & 64.74\% & 74.77\% \\
Inserted bases per 100 aligned bases (including indels) & 4.79\% & 4.03\% & 4.59\% \\
Deleted bases per 100 aligned bases (including indels) & 11.62\% & 14.70\% & 8.98\% \\
Substitutions per 100 aligned bases (including indels) & 17.00\% & 16.53\% & 11.66\% \\
Mean insertion size & 1.56 & 1.50 & 1.53 \\
Mean deletion size & 1.72 & 1.87 & 1.69 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_deletions.png}
\end{figure}
\subsection*{Control sequence read identity}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_read_fraction_vs_alignment_identity_scatter.png}
\end{figure}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_percent_aligned_vs_length_scatter.png}
\end{figure}
\subsection*{Control sequence perfect kmers}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_longest_perfect_vs_length_scatter.png}
\end{figure}
\subsection*{Control sequence coverage}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_gc.png}
\end{figure}
\subsection*{Control sequence 5-mer analysis}
\subsection*{Under-represented 5-mers}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{7pt}{9pt}\selectfont
\begin{tabular}{|c|c c c c|c c c c|c c c c|}
\cline{1-13}
 & \multicolumn{4}{c|}{Template} & \multicolumn{4}{c|}{Complement} & \multicolumn{4}{c|}{2D} \\
Rank & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% \\
\cline{1-13}
1 & TTTTT & 0.759 & 0.126 & -0.633 & TTTTT & 0.759 & 0.077 & -0.681 & TTTTT & 0.759 & 0.045 & -0.714 \\
2 & AAAAA & 0.478 & 0.091 & -0.387 & AAAAA & 0.478 & 0.045 & -0.433 & AAAAA & 0.478 & 0.047 & -0.430 \\
3 & TGATG & 0.393 & 0.136 & -0.257 & AAAAC & 0.337 & 0.100 & -0.237 & TGATG & 0.393 & 0.156 & -0.238 \\
4 & AAAAC & 0.337 & 0.120 & -0.217 & TGATG & 0.393 & 0.177 & -0.216 & AAAAC & 0.337 & 0.143 & -0.194 \\
5 & GATGT & 0.309 & 0.098 & -0.211 & GATGT & 0.309 & 0.102 & -0.207 & GATGT & 0.309 & 0.124 & -0.185 \\
6 & CTGAT & 0.309 & 0.110 & -0.199 & GCAAT & 0.309 & 0.126 & -0.183 & CTGAT & 0.309 & 0.140 & -0.169 \\
7 & AATAT & 0.309 & 0.134 & -0.175 & TTATC & 0.309 & 0.133 & -0.176 & CTTTT & 0.253 & 0.098 & -0.155 \\
8 & GCAAT & 0.309 & 0.135 & -0.174 & AACAA & 0.281 & 0.106 & -0.175 & TTATC & 0.309 & 0.157 & -0.152 \\
9 & GCTGA & 0.281 & 0.111 & -0.170 & AATAT & 0.309 & 0.139 & -0.170 & GCTGA & 0.281 & 0.135 & -0.146 \\
10 & TAATA & 0.281 & 0.113 & -0.168 & AGAAA & 0.281 & 0.111 & -0.170 & GCAAT & 0.309 & 0.164 & -0.145 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-3mm}
\subsection*{Over-represented 5-mers}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{7pt}{9pt}\selectfont
\begin{tabular}{|c|c c c c|c c c c|c c c c|}
\cline{1-13}
 & \multicolumn{4}{c|}{Template} & \multicolumn{4}{c|}{Complement} & \multicolumn{4}{c|}{2D} \\
Rank & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% \\
\cline{1-13}
1 & CTTTG & 0.028 & 0.148 & 0.120 & CTTTG & 0.028 & 0.159 & 0.130 & GCATC & 0.084 & 0.185 & 0.100 \\
2 & ATCTA & 0.000 & 0.119 & 0.119 & TACTT & 0.000 & 0.126 & 0.126 & TCAGC & 0.028 & 0.127 & 0.099 \\
3 & TACTT & 0.000 & 0.114 & 0.114 & GAGGA & 0.000 & 0.122 & 0.122 & CATCT & 0.000 & 0.096 & 0.096 \\
4 & CATCT & 0.000 & 0.113 & 0.113 & TGCTT & 0.084 & 0.201 & 0.117 & AACCA & 0.028 & 0.121 & 0.093 \\
5 & CCCCA & 0.000 & 0.108 & 0.108 & ACCCC & 0.000 & 0.116 & 0.116 & ATCTA & 0.000 & 0.092 & 0.092 \\
6 & GCTCC & 0.000 & 0.107 & 0.107 & GGAAT & 0.112 & 0.229 & 0.116 & GTCGA & 0.000 & 0.090 & 0.090 \\
7 & TCTAC & 0.000 & 0.107 & 0.107 & CTTAC & 0.000 & 0.112 & 0.112 & CAGCA & 0.056 & 0.145 & 0.089 \\
8 & ACCCC & 0.000 & 0.104 & 0.104 & TCAGC & 0.028 & 0.139 & 0.111 & CCCGC & 0.000 & 0.089 & 0.089 \\
9 & ACTCT & 0.000 & 0.100 & 0.100 & TATAC & 0.000 & 0.111 & 0.111 & TCTAC & 0.000 & 0.088 & 0.088 \\
10 & TCAGC & 0.028 & 0.127 & 0.099 & GCCGA & 0.000 & 0.110 & 0.110 & CTTTG & 0.028 & 0.116 & 0.088 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_kmer_scatter.png} \\
\end{figure}
\subsection*{Control sequence GC content}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Control_sequence/Control_sequence_2D_GC_hist.png}
\clearpage
\subsection*{Escherichia coli error analysis}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{9pt}{11pt}\selectfont
\begin{tabular}{l c c c}
 & Template & Complement & 2D \\
Overall base identity (excluding indels) & 57.87\% & 54.03\% & 75.22\% \\
Aligned base identity (excluding indels) & 78.99\% & 79.84\% & 86.66\% \\
Identical bases per 100 aligned bases (including indels) & 65.31\% & 64.49\% & 74.81\% \\
Inserted bases per 100 aligned bases (including indels) & 4.78\% & 4.11\% & 4.60\% \\
Deleted bases per 100 aligned bases (including indels) & 12.54\% & 15.12\% & 9.08\% \\
Substitutions per 100 aligned bases (including indels) & 17.37\% & 16.28\% & 11.51\% \\
Mean insertion size & 1.57 & 1.53 & 1.56 \\
Mean deletion size & 1.76 & 1.90 & 1.72 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_deletions.png}
\end{figure}
\subsection*{Escherichia coli read identity}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_read_fraction_vs_alignment_identity_scatter.png}
\end{figure}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_percent_aligned_vs_length_scatter.png}
\end{figure}
\subsection*{Escherichia coli perfect kmers}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_longest_perfect_vs_length_scatter.png}
\end{figure}
\subsection*{Escherichia coli coverage}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_gc.png}
\end{figure}
\subsection*{Escherichia coli 5-mer analysis}
\subsection*{Under-represented 5-mers}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{7pt}{9pt}\selectfont
\begin{tabular}{|c|c c c c|c c c c|c c c c|}
\cline{1-13}
 & \multicolumn{4}{c|}{Template} & \multicolumn{4}{c|}{Complement} & \multicolumn{4}{c|}{2D} \\
Rank & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% \\
\cline{1-13}
1 & AAAAA & 0.247 & 0.063 & -0.184 & AAAAA & 0.247 & 0.038 & -0.209 & TTTTT & 0.251 & 0.033 & -0.218 \\
2 & CGCTG & 0.259 & 0.076 & -0.183 & CGCCA & 0.288 & 0.083 & -0.205 & AAAAA & 0.247 & 0.036 & -0.211 \\
3 & TTTTT & 0.251 & 0.088 & -0.163 & TTTTT & 0.251 & 0.057 & -0.194 & CGCCA & 0.288 & 0.173 & -0.115 \\
4 & GCTGG & 0.279 & 0.120 & -0.160 & CGCTG & 0.259 & 0.110 & -0.149 & GCTGG & 0.279 & 0.166 & -0.113 \\
5 & CGCCA & 0.288 & 0.130 & -0.158 & CTGGC & 0.278 & 0.133 & -0.145 & CGCTG & 0.259 & 0.146 & -0.113 \\
6 & CTGGC & 0.278 & 0.141 & -0.137 & CGCGC & 0.201 & 0.064 & -0.137 & GCCAG & 0.280 & 0.170 & -0.110 \\
7 & GCCAG & 0.280 & 0.150 & -0.130 & TGGCG & 0.275 & 0.139 & -0.137 & TGGCG & 0.275 & 0.172 & -0.104 \\
8 & CCAGC & 0.289 & 0.163 & -0.126 & CCAGC & 0.289 & 0.156 & -0.133 & CCAGC & 0.289 & 0.189 & -0.100 \\
9 & TGGCG & 0.275 & 0.151 & -0.125 & GCCAG & 0.280 & 0.149 & -0.131 & CTGGC & 0.278 & 0.183 & -0.096 \\
10 & CAGCA & 0.261 & 0.154 & -0.108 & GCGCA & 0.202 & 0.074 & -0.128 & AAAAT & 0.195 & 0.105 & -0.090 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-3mm}
\subsection*{Over-represented 5-mers}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{7pt}{9pt}\selectfont
\begin{tabular}{|c|c c c c|c c c c|c c c c|}
\cline{1-13}
 & \multicolumn{4}{c|}{Template} & \multicolumn{4}{c|}{Complement} & \multicolumn{4}{c|}{2D} \\
Rank & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% & kmer & Ref \% & Read \% & Diff \% \\
\cline{1-13}
1 & ACCCC & 0.040 & 0.127 & 0.086 & ACCCC & 0.040 & 0.132 & 0.091 & CTAGA & 0.003 & 0.063 & 0.060 \\
2 & CCTAG & 0.003 & 0.088 & 0.085 & TAGGA & 0.012 & 0.097 & 0.085 & TCTAG & 0.003 & 0.061 & 0.058 \\
3 & TAGGA & 0.012 & 0.096 & 0.084 & GGAAT & 0.089 & 0.163 & 0.073 & TCTAA & 0.025 & 0.080 & 0.055 \\
4 & GGATT & 0.098 & 0.177 & 0.078 & TACCC & 0.073 & 0.146 & 0.072 & CTCGT & 0.042 & 0.097 & 0.055 \\
5 & ATCTA & 0.033 & 0.111 & 0.078 & TGCTT & 0.099 & 0.169 & 0.070 & CCTCC & 0.033 & 0.088 & 0.055 \\
6 & TCCGT & 0.066 & 0.144 & 0.078 & TCCTA & 0.013 & 0.083 & 0.070 & TAGAT & 0.035 & 0.089 & 0.054 \\
7 & CCCCC & 0.033 & 0.108 & 0.075 & CCTAG & 0.003 & 0.072 & 0.070 & GGGTC & 0.040 & 0.094 & 0.053 \\
8 & CCCCG & 0.055 & 0.130 & 0.075 & CCTAT & 0.028 & 0.097 & 0.069 & ATCTA & 0.033 & 0.085 & 0.053 \\
9 & CTCCC & 0.040 & 0.113 & 0.073 & ATCTA & 0.033 & 0.099 & 0.066 & TTAGA & 0.026 & 0.079 & 0.053 \\
10 & CCCCA & 0.064 & 0.136 & 0.072 & ACCTA & 0.027 & 0.092 & 0.065 & CCGTA & 0.079 & 0.130 & 0.051 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_kmer_scatter.png} \\
\end{figure}
\subsection*{Escherichia coli GC content}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/Escherichia_coli/Escherichia_coli_2D_GC_hist.png}
\clearpage
\subsection*{All reference 21mer analysis}
\vspace{-3mm}
\begin{figure}[H]
\centering
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_Template_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_Complement_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/all_2D_21mers.png}
\end{figure}
\subsection*{All reference substitutions}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{8pt}{10pt}\selectfont
\begin{tabular}{|c c|c c c c|c c c c|c c c c|}
\hline
 & & \multicolumn{4}{c|}{Template substituted \%} & \multicolumn{4}{c|}{Complement substituted \%} & \multicolumn{4}{c|}{2D substituted \%} \\
 & & a & c & g & t & a & c & g & t & a & c & g & t \\
\hline
\multirow{4}{*}{\rotatebox[origin=c]{90}{Reference}} & A & 0.00 & 9.36 & 9.21 & 5.16 & 0.00 & 9.22 & 8.82 & 5.36 & 0.00 & 9.47 & 8.92 & 4.84\\
 & C & 8.23 & 0.00 & 8.56 & 9.35 & 8.68 & 0.00 & 8.28 & 9.21 & 8.34 & 0.00 & 9.56 & 8.37\\
 & G & 9.14 & 8.72 & 0.00 & 7.98 & 8.58 & 8.60 & 0.00 & 8.67 & 8.45 & 9.90 & 0.00 & 8.18\\
 & T & 5.62 & 9.55 & 9.14 & 0.00 & 5.78 & 9.41 & 9.39 & 0.00 & 5.11 & 9.29 & 9.56 & 0.00\\
\hline
\end{tabular}
}
\end{table}
\subsection*{Kmer motifs before errors}
\subsection*{3-mer error motif analysis}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{6pt}{8pt}\selectfont
\tabcolsep=0.15cm
\begin{tabular}{|c|c c c|c c c|c c c|c}
\cline{1-10}
 & \multicolumn{3}{c|}{Template} & \multicolumn{3}{c|}{Complement} & \multicolumn{3}{c|}{2D} & \\
Rank & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & \\
\cline{1-10}
1 & TTC (3.22\%) & TTC (3.46\%) & AAA (4.44\%) & AAA (2.92\%) & AAA (3.06\%) & AAA (4.42\%) & AAA (3.17\%) & AAA (2.88\%) & AAA (4.19\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & AAA (2.94\%) & TGC (3.06\%) & TTC (3.56\%) & TTC (2.88\%) & TGC (2.88\%) & GCA (3.42\%) & GCA (3.06\%) & TGC (2.71\%) & GCA (3.47\%)\\
3 & GCA (2.76\%) & AAA (2.97\%) & GCA (3.22\%) & TGC (2.81\%) & TTC (2.75\%) & GAA (3.38\%) & TTC (2.79\%) & GCA (2.55\%) & GAA (3.15\%)\\
4 & TGC (2.64\%) & GCA (2.78\%) & GAA (3.09\%) & GCA (2.74\%) & GCA (2.66\%) & TTC (3.11\%) & TCA (2.60\%) & GAA (2.47\%) & TTT (3.00\%)\\
5 & ATC (2.58\%) & TCA (2.37\%) & TTT (2.84\%) & GAA (2.52\%) & GAA (2.61\%) & TTT (2.67\%) & GAA (2.57\%) & TTC (2.43\%) & TTC (2.86\%)\\
6 & TCA (2.56\%) & GAA (2.36\%) & AAT (2.76\%) & TCA (2.40\%) & GGC (2.48\%) & AAT (2.53\%) & AAT (2.49\%) & TCA (2.43\%) & AAT (2.84\%)\\
7 & TTT (2.55\%) & AAT (2.31\%) & TGC (2.46\%) & AAT (2.39\%) & AAT (2.40\%) & TCA (2.43\%) & TGC (2.35\%) & CAG (2.21\%) & GTT (2.65\%)\\
8 & AAT (2.41\%) & ATC (2.22\%) & TCA (2.40\%) & ATC (2.34\%) & TCA (2.32\%) & TGC (2.41\%) & TTT (2.32\%) & GCG (2.17\%) & TCA (2.33\%)\\
9 & GAA (2.33\%) & GCC (2.22\%) & CAA (2.37\%) & TTT (2.33\%) & CAG (2.20\%) & CAA (2.30\%) & ATC (2.30\%) & GGC (2.14\%) & GCC (2.12\%)\\
10 & GCC (2.02\%) & AAC (2.14\%) & ATC (2.12\%) & CAG (2.23\%) & ATC (2.13\%) & ATC (2.13\%) & GCG (2.05\%) & ATC (2.09\%) & TGC (2.10\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_top_k3.png} \\
\cline{1-10}
-10 & CTC (0.96\%) & ACT (0.95\%) & CGA (0.89\%) & AGA (0.98\%) & GGA (0.95\%) & AGT (0.90\%) & CTT (0.98\%) & GTA (1.02\%) & GTA (0.97\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & CGA (0.93\%) & GGG (0.94\%) & AGA (0.88\%) & CGA (0.97\%) & AGG (0.93\%) & CTT (0.90\%) & CGA (0.96\%) & GGG (1.00\%) & CCC (0.97\%)\\
-8 & GGA (0.89\%) & AGT (0.89\%) & GGT (0.86\%) & GGA (0.86\%) & CCT (0.92\%) & CCT (0.86\%) & GAG (0.90\%) & CCT (0.96\%) & ACT (0.90\%)\\
-7 & AGA (0.85\%) & GAG (0.88\%) & AGG (0.85\%) & CTC (0.82\%) & CGA (0.91\%) & CTC (0.86\%) & AGA (0.86\%) & AGA (0.92\%) & GAG (0.86\%)\\
-6 & CCC (0.85\%) & CTT (0.85\%) & GGG (0.83\%) & CCC (0.78\%) & CTC (0.89\%) & ACT (0.80\%) & GGA (0.85\%) & ACT (0.88\%) & CTT (0.82\%)\\
-5 & GAG (0.82\%) & AGA (0.76\%) & AGT (0.79\%) & AGG (0.75\%) & ACT (0.89\%) & AGG (0.79\%) & AGG (0.78\%) & CTT (0.87\%) & CGA (0.73\%)\\
-4 & AGG (0.70\%) & CGA (0.76\%) & CTT (0.78\%) & GAG (0.75\%) & GAG (0.89\%) & GGG (0.75\%) & CCC (0.78\%) & CGA (0.83\%) & GGA (0.71\%)\\
-3 & GGG (0.69\%) & GGA (0.73\%) & GAG (0.72\%) & GGG (0.60\%) & GGG (0.75\%) & GAG (0.65\%) & GGG (0.69\%) & GGA (0.79\%) & AGA (0.68\%)\\
-2 & CTA (0.55\%) & TAG (0.61\%) & TAG (0.44\%) & CTA (0.58\%) & TAG (0.61\%) & TAG (0.42\%) & TAG (0.62\%) & TAG (0.71\%) & TAG (0.55\%)\\
-1 & TAG (0.50\%) & CTA (0.52\%) & CTA (0.37\%) & TAG (0.49\%) & CTA (0.47\%) & CTA (0.42\%) & CTA (0.62\%) & CTA (0.64\%) & CTA (0.44\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_bottom_k3.png} \\
\cline{1-10}
\end{tabular}
}
\end{table}
\vspace{-9mm}
{\fontsize{8}{8}\textsf{Kmer space for 3-mers: 64 \hspace{5mm} Random chance for any given 3-mer: 1.56\%}}
\vspace{5mm}
\subsection*{4-mer error motif analysis}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{6pt}{8pt}\selectfont
\tabcolsep=0.15cm
\begin{tabular}{|c|c c c|c c c|c c c|c}
\cline{1-10}
 & \multicolumn{3}{c|}{Template} & \multicolumn{3}{c|}{Complement} & \multicolumn{3}{c|}{2D} & \\
Rank & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & \\
\cline{1-10}
1 & TTTC (1.00\%) & TTTC (1.22\%) & AAAA (1.58\%) & CAAA (0.89\%) & CAAA (0.96\%) & CAAA (1.25\%) & CAAA (0.96\%) & CAAA (0.86\%) & AAAA (1.26\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & TTTT (0.97\%) & TTGC (0.91\%) & TTTC (1.28\%) & CTGC (0.85\%) & TGGC (0.93\%) & AAAA (1.24\%) & GAAA (0.87\%) & GGAA (0.86\%) & GAAA (1.07\%)\\
3 & GAAA (0.93\%) & TTCA (0.89\%) & GAAA (1.20\%) & ATCA (0.85\%) & TTGC (0.92\%) & GAAA (1.02\%) & AACA (0.83\%) & TTCA (0.83\%) & TGCA (1.03\%)\\
4 & AAAA (0.92\%) & GAAA (0.88\%) & TTTT (1.03\%) & TTGC (0.82\%) & CTGC (0.88\%) & TGAA (1.00\%) & TGCA (0.82\%) & TGGC (0.80\%) & GGCA (1.00\%)\\
5 & TTCA (0.87\%) & AAAA (0.87\%) & GCAA (0.97\%) & AAAA (0.78\%) & CAGC (0.88\%) & AGAA (0.95\%) & ATCA (0.80\%) & ATGC (0.80\%) & CAAA (0.97\%)\\
6 & TTGC (0.84\%) & TGCC (0.86\%) & CAAA (0.94\%) & GAAA (0.77\%) & CGGC (0.86\%) & AGCA (0.93\%) & AAAA (0.79\%) & ATCA (0.77\%) & GGAA (0.96\%)\\
7 & ATCA (0.83\%) & CTGC (0.86\%) & TGAA (0.90\%) & CAGC (0.76\%) & TTCC (0.82\%) & TTTC (0.91\%) & TTCA (0.79\%) & CAGC (0.77\%) & TGTT (0.92\%)\\
8 & GTTT (0.80\%) & TTCC (0.86\%) & GTTT (0.89\%) & TTTC (0.76\%) & TTCA (0.80\%) & TAAA (0.91\%) & TGAA (0.79\%) & GAAA (0.76\%) & TTTC (0.91\%)\\
9 & AACG (0.79\%) & TGGC (0.81\%) & TGCA (0.88\%) & ATTC (0.76\%) & AGCA (0.79\%) & ATCA (0.88\%) & GGCA (0.77\%) & AGCA (0.76\%) & TTTT (0.91\%)\\
10 & TGCA (0.79\%) & ATGC (0.79\%) & AAAT (0.87\%) & TGGC (0.75\%) & TTTC (0.79\%) & TGCA (0.86\%) & TTTC (0.76\%) & CTGC (0.76\%) & CGTT (0.87\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_top_k4.png} \\
\cline{1-10}
-10 & TAGT (0.13\%) & CGAG (0.12\%) & GGGT (0.11\%) & TAGT (0.13\%) & GGGG (0.12\%) & TCTA (0.11\%) & CTTG (0.15\%) & ACTA (0.14\%) & CGGA (0.12\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & GAGG (0.13\%) & CTAA (0.12\%) & CTAT (0.11\%) & TAGA (0.13\%) & CGAG (0.12\%) & GTGT (0.11\%) & CGAG (0.15\%) & CCCT (0.14\%) & ACTA (0.12\%)\\
-8 & TCTA (0.13\%) & TCTA (0.11\%) & TAGT (0.11\%) & CCCT (0.12\%) & CTAT (0.11\%) & CTAT (0.09\%) & GGAC (0.14\%) & ACCT (0.14\%) & CCCT (0.11\%)\\
-7 & CGAG (0.12\%) & CTAT (0.11\%) & ACTA (0.10\%) & GAGG (0.11\%) & ACCT (0.11\%) & GGAC (0.09\%) & CCCC (0.14\%) & CCGA (0.14\%) & CTTG (0.11\%)\\
-6 & AGGG (0.12\%) & TAGT (0.11\%) & CGAG (0.09\%) & AGGG (0.11\%) & ACTA (0.11\%) & ACTA (0.09\%) & TCTA (0.13\%) & CCCC (0.13\%) & CTAT (0.11\%)\\
-5 & CCTA (0.09\%) & TAGG (0.10\%) & TCTA (0.08\%) & CCTA (0.11\%) & TAGA (0.11\%) & CCCT (0.08\%) & CTAT (0.13\%) & CCTA (0.12\%) & TCTA (0.10\%)\\
-4 & GGAC (0.08\%) & GGAC (0.09\%) & GGAC (0.07\%) & GGAC (0.10\%) & CCCC (0.10\%) & CGAG (0.08\%) & TAGA (0.09\%) & CTAT (0.12\%) & TAGA (0.08\%)\\
-3 & TAGA (0.08\%) & CCTA (0.08\%) & TAGG (0.06\%) & CGAG (0.10\%) & TAGG (0.10\%) & TAGG (0.06\%) & CCTA (0.09\%) & TAGG (0.12\%) & TAGG (0.07\%)\\
-2 & TAGG (0.06\%) & TAGA (0.06\%) & CCTA (0.05\%) & TAGG (0.08\%) & CCTA (0.06\%) & CCTA (0.05\%) & TAGG (0.06\%) & TAGA (0.09\%) & CCTA (0.06\%)\\
-1 & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.02\%) & CTAG (0.01\%) & CTAG (0.04\%) & CTAG (0.02\%) & CTAG (0.02\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_bottom_k4.png} \\
\cline{1-10}
\end{tabular}
}
\end{table}
\vspace{-9mm}
{\fontsize{8}{8}\textsf{Kmer space for 4-mers: 256 \hspace{5mm} Random chance for any given 4-mer: 0.39\%}}
\vspace{5mm}
\subsection*{5-mer error motif analysis}
\vspace{-3mm}
\begin{table}[H]
{\footnotesize
\fontsize{6pt}{8pt}\selectfont
\tabcolsep=0.15cm
\begin{tabular}{|c|c c c|c c c|c c c|c}
\cline{1-10}
 & \multicolumn{3}{c|}{Template} & \multicolumn{3}{c|}{Complement} & \multicolumn{3}{c|}{2D} & \\
Rank & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & Insertion & Deletion & Substitution & \\
\cline{1-10}
1 & TTATC (0.38\%) & GATGC (0.38\%) & GAAAA (0.54\%) & CAGCA (0.35\%) & CAGCA (0.38\%) & CAGCA (0.45\%) & TCAAA (0.33\%) & GATGC (0.42\%) & GAAAA (0.42\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & CGTTT (0.36\%) & ATTTC (0.35\%) & AGAAA (0.43\%) & CATCA (0.30\%) & CTGGC (0.36\%) & GAAAA (0.43\%) & CGTCA (0.31\%) & TATCG (0.37\%) & TGGCA (0.41\%)\\
3 & GTTGC (0.32\%) & CTGGC (0.35\%) & CAAAA (0.39\%) & CGTTT (0.29\%) & ACAAA (0.36\%) & ACAAA (0.42\%) & GCAAT (0.31\%) & ACAAA (0.37\%) & CAAAA (0.39\%)\\
4 & ATTTT (0.32\%) & CAGCA (0.33\%) & CGTTT (0.35\%) & ACAAA (0.29\%) & GATGC (0.35\%) & AAGAA (0.38\%) & GCAAA (0.30\%) & CTGGC (0.35\%) & AGAAA (0.38\%)\\
5 & AGAAA (0.32\%) & GTTTC (0.33\%) & TAAAA (0.35\%) & TTATC (0.29\%) & TGATG (0.31\%) & CAGAA (0.36\%) & CAGCA (0.30\%) & TTATT (0.32\%) & GCAAT (0.35\%)\\
6 & CAAAA (0.31\%) & TTTCA (0.32\%) & ATTTC (0.34\%) & GCTGC (0.28\%) & AATCA (0.31\%) & AATCA (0.35\%) & TTGCA (0.30\%) & GCCAG (0.30\%) & CAGCA (0.34\%)\\
7 & TTTCT (0.31\%) & TGTTC (0.32\%) & GCAAT (0.34\%) & AATCA (0.28\%) & ATTCC (0.30\%) & AGAAA (0.35\%) & TGGCA (0.29\%) & TGGAA (0.29\%) & CGGCA (0.33\%)\\
8 & CTGGC (0.30\%) & GCCAG (0.32\%) & CAGCA (0.34\%) & GATGC (0.28\%) & GCGGC (0.30\%) & ATGAA (0.34\%) & CGCCA (0.28\%) & CATCA (0.29\%) & AGGAA (0.33\%)\\
9 & GAAAA (0.30\%) & TTTGC (0.32\%) & TTTTC (0.33\%) & CTGGC (0.28\%) & GCAGC (0.30\%) & CAAAA (0.33\%) & AGAAA (0.28\%) & TTTCA (0.29\%) & CTGCA (0.32\%)\\
10 & GTTTT (0.29\%) & TATCG (0.31\%) & CTGAA (0.33\%) & GCAAA (0.27\%) & ATTGC (0.29\%) & GCAAA (0.33\%) & TGTTC (0.28\%) & TCTTT (0.28\%) & ACAAA (0.31\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_top_k5.png} \\
\cline{1-10}
-10 & TAGGG (0.01\%) & TAGGG (0.01\%) & CTTAG (0.01\%) & GGACC (0.01\%) & CCCCT (0.01\%) & TAGGT (0.01\%) & CTTGG (0.01\%) & TCCTA (0.01\%) & CCCTA (0.01\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & CTAGT (0.01\%) & CCCTA (0.01\%) & TAGGG (0.01\%) & TAGGG (0.01\%) & ACCTA (0.01\%) & CCCTA (0.01\%) & TAGGG (0.01\%) & CCCTA (0.01\%) & GCTAG (0.01\%)\\
-8 & GCTAG (0.00\%) & GCTAG (0.00\%) & GCTAG (0.00\%) & CTAGA (0.01\%) & CCCTA (0.01\%) & GCTAG (0.00\%) & CCCTA (0.01\%) & GCTAG (0.01\%) & TTAGA (0.01\%)\\
-7 & GGACC (0.00\%) & CTAGA (0.00\%) & ACTAG (0.00\%) & GCTAG (0.01\%) & CTAGA (0.00\%) & CTAGT (0.00\%) & GGACC (0.01\%) & CTAGA (0.01\%) & CTAGA (0.00\%)\\
-6 & CCTAG (0.00\%) & ACTAG (0.00\%) & CTAGC (0.00\%) & CTAGT (0.01\%) & CTAGT (0.00\%) & CTAGA (0.00\%) & CTAGA (0.01\%) & ACTAG (0.00\%) & CCTAG (0.00\%)\\
-5 & CTAGA (0.00\%) & CCTAG (0.00\%) & CCTAG (0.00\%) & CTAGC (0.00\%) & CTAGC (0.00\%) & ACTAG (0.00\%) & CTAGT (0.00\%) & CTAGC (0.00\%) & CTAGC (0.00\%)\\
-4 & CTAGC (0.00\%) & CTAGC (0.00\%) & CTAGT (0.00\%) & CCTAG (0.00\%) & ACTAG (0.00\%) & CTAGC (0.00\%) & CTAGC (0.00\%) & CTAGT (0.00\%) & TCTAG (0.00\%)\\
-3 & ACTAG (0.00\%) & CTAGT (0.00\%) & CTAGA (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & CTAGG (0.00\%) & ACTAG (0.00\%) & TCTAG (0.00\%) & CTAGT (0.00\%)\\
-2 & CTAGG (0.00\%) & TCTAG (0.00\%) & CTAGG (0.00\%) & ACTAG (0.00\%) & TCTAG (0.00\%) & CCTAG (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & CTAGG (0.00\%)\\
-1 & TCTAG (0.00\%) & CTAGG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%) & CTAGG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%) & CTAGG (0.00\%) & ACTAG (0.00\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_insertion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_deletion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/ZF-screens_MARC_phase_1a_e_coli_run1/graphs/motifs/logo_substitution_2D_bottom_k5.png} \\
\cline{1-10}
\end{tabular}
}
\end{table}
\vspace{-9mm}
{\fontsize{8}{8}\textsf{Kmer space for 5-mers: 1024 \hspace{5mm} Random chance for any given 5-mer: 0.10\%}}
\vspace{5mm}
\end{document}
\end{document}
