\documentclass[a4paper,11pt,oneside]{article}
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\begin{document}
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\section*{\large{NanoOK report for JOGrady\_MARC1b\_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 & 12258 & 0  \\
Complement & 12258 & 0  \\
2D & 12258 & 0  \\
\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 & 12258 & 68123762 & 5557.49 & 32654 & 182 & 6671 & 4001 & 3656 & 9153 \\
Complement & 12258 & 68119862 & 5557.18 & 31734 & 151 & 6677 & 3997 & 3688 & 9149 \\
2D & 12258 & 69409047 & 5662.35 & 32099 & 163 & 6804 & 3996 & 3720 & 9144 \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{figure}[H]
\centering
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/all_Template_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/all_Complement_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 & 12258 & \\
Number of reads with alignments & 11682 & (95.30\%) \\
Number of reads without alignments & 576 & (4.70\%) \\
\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 & 839 & 6.84 & 3137.38 & 2796046 & 785.41 & 51 \\
Escherichia coli & 4641652 & 10843 & 88.46 & 5992.03 & 70209063 & 15.13 & 76 \\
\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 & 12258 & \\
Number of reads with alignments & 11700 & (95.45\%) \\
Number of reads without alignments & 558 & (4.55\%) \\
\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 & 847 & 6.91 & 3090.14 & 2706387 & 760.22 & 51 \\
Escherichia coli & 4641652 & 10853 & 88.54 & 5988.96 & 69762992 & 15.03 & 66 \\
\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 & 12258 & \\
Number of reads with alignments & 11807 & (96.32\%) \\
Number of reads without alignments & 451 & (3.68\%) \\
\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 & 854 & 6.97 & 3135.98 & 2804996 & 787.92 & 213 \\
Escherichia coli & 4641652 & 10953 & 89.35 & 6052.33 & 69678795 & 15.01 & 209 \\
\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) & 72.17\% & 70.52\% & 88.54\% \\
Aligned base identity (excluding indels) & 79.91\% & 81.22\% & 93.21\% \\
Identical bases per 100 aligned bases (including indels) & 67.94\% & 68.20\% & 84.53\% \\
Inserted bases per 100 aligned bases (including indels) & 4.74\% & 5.25\% & 2.86\% \\
Deleted bases per 100 aligned bases (including indels) & 10.23\% & 10.79\% & 6.45\% \\
Substitutions per 100 aligned bases (including indels) & 17.08\% & 15.77\% & 6.16\% \\
Mean insertion size & 1.54 & 1.59 & 1.45 \\
Mean deletion size & 1.57 & 1.67 & 1.60 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 & 0.136 & -0.623 & TTTTT & 0.759 & 0.110 & -0.649 & TTTTT & 0.759 & 0.056 & -0.703 \\
2 & AAAAA & 0.478 & 0.109 & -0.369 & AAAAA & 0.478 & 0.091 & -0.387 & AAAAA & 0.478 & 0.068 & -0.409 \\
3 & TGATG & 0.393 & 0.133 & -0.260 & AAAAC & 0.337 & 0.151 & -0.186 & TGATG & 0.393 & 0.176 & -0.217 \\
4 & GATGT & 0.309 & 0.098 & -0.211 & GCAAT & 0.309 & 0.139 & -0.171 & GATGT & 0.309 & 0.144 & -0.165 \\
5 & AAAAC & 0.337 & 0.133 & -0.204 & GATGT & 0.309 & 0.139 & -0.170 & CTGAT & 0.309 & 0.144 & -0.165 \\
6 & CTGAT & 0.309 & 0.122 & -0.187 & GTCAG & 0.281 & 0.113 & -0.168 & GCTGA & 0.281 & 0.131 & -0.150 \\
7 & AATAT & 0.309 & 0.133 & -0.176 & TGATG & 0.393 & 0.227 & -0.167 & CTTTT & 0.253 & 0.106 & -0.147 \\
8 & GCAAT & 0.309 & 0.136 & -0.173 & TGAAG & 0.253 & 0.092 & -0.161 & AAAAC & 0.337 & 0.195 & -0.142 \\
9 & AGTAA & 0.253 & 0.084 & -0.169 & AACAA & 0.281 & 0.126 & -0.155 & TGTGA & 0.225 & 0.091 & -0.134 \\
10 & TGAAG & 0.253 & 0.097 & -0.156 & AGTAA & 0.253 & 0.102 & -0.151 & TTATC & 0.309 & 0.175 & -0.134 \\
\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 & 0.162 & 0.134 & ACCCC & 0.000 & 0.127 & 0.127 & TCAGC & 0.028 & 0.172 & 0.143 \\
2 & TCTTA & 0.000 & 0.119 & 0.119 & GAGGA & 0.000 & 0.126 & 0.126 & CATCA & 0.112 & 0.254 & 0.142 \\
3 & CATCT & 0.000 & 0.118 & 0.118 & CCCCA & 0.000 & 0.119 & 0.119 & ATCAG & 0.056 & 0.195 & 0.139 \\
4 & GCTCC & 0.000 & 0.110 & 0.110 & GTATC & 0.000 & 0.110 & 0.110 & AACCA & 0.028 & 0.155 & 0.127 \\
5 & CGAGA & 0.000 & 0.109 & 0.109 & TATAC & 0.000 & 0.106 & 0.106 & CATCT & 0.000 & 0.117 & 0.117 \\
6 & TCAGC & 0.028 & 0.135 & 0.107 & ACTCT & 0.000 & 0.105 & 0.105 & GCATC & 0.084 & 0.201 & 0.117 \\
7 & CCCGC & 0.000 & 0.105 & 0.105 & TACTT & 0.000 & 0.102 & 0.102 & ACCAA & 0.028 & 0.141 & 0.113 \\
8 & TCTAC & 0.000 & 0.104 & 0.104 & TGCGA & 0.028 & 0.130 & 0.102 & CAGCA & 0.056 & 0.168 & 0.112 \\
9 & GCGAA & 0.028 & 0.130 & 0.102 & CTTTG & 0.028 & 0.129 & 0.101 & TACAT & 0.028 & 0.139 & 0.111 \\
10 & GTATC & 0.000 & 0.101 & 0.101 & CGAGA & 0.000 & 0.098 & 0.098 & ACATA & 0.028 & 0.132 & 0.104 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Control_sequence/Control_sequence_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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) & 72.60\% & 72.64\% & 88.77\% \\
Aligned base identity (excluding indels) & 79.45\% & 80.86\% & 93.02\% \\
Identical bases per 100 aligned bases (including indels) & 67.18\% & 67.68\% & 84.45\% \\
Inserted bases per 100 aligned bases (including indels) & 5.20\% & 5.70\% & 3.16\% \\
Deleted bases per 100 aligned bases (including indels) & 10.24\% & 10.60\% & 6.05\% \\
Substitutions per 100 aligned bases (including indels) & 17.37\% & 16.02\% & 6.34\% \\
Mean insertion size & 1.59 & 1.62 & 1.49 \\
Mean deletion size & 1.60 & 1.65 & 1.55 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 & CGCTG & 0.259 & 0.094 & -0.165 & CGCCA & 0.288 & 0.097 & -0.191 & TTTTT & 0.251 & 0.036 & -0.214 \\
2 & AAAAA & 0.247 & 0.090 & -0.157 & TTTTT & 0.251 & 0.080 & -0.171 & AAAAA & 0.247 & 0.042 & -0.205 \\
3 & TTTTT & 0.251 & 0.099 & -0.152 & AAAAA & 0.247 & 0.079 & -0.168 & CGCCA & 0.288 & 0.204 & -0.084 \\
4 & CGCCA & 0.288 & 0.147 & -0.141 & CACCA & 0.184 & 0.051 & -0.133 & CAAAA & 0.169 & 0.092 & -0.078 \\
5 & GCTGG & 0.279 & 0.139 & -0.140 & CCAGC & 0.289 & 0.159 & -0.130 & AAAAT & 0.195 & 0.118 & -0.077 \\
6 & GCCAG & 0.280 & 0.153 & -0.127 & CAGCA & 0.261 & 0.133 & -0.129 & TGGCG & 0.275 & 0.203 & -0.072 \\
7 & CCAGC & 0.289 & 0.172 & -0.116 & CGCTG & 0.259 & 0.131 & -0.128 & GCCAG & 0.280 & 0.211 & -0.069 \\
8 & CTGGC & 0.278 & 0.163 & -0.115 & CTGGC & 0.278 & 0.154 & -0.125 & CGCTG & 0.259 & 0.191 & -0.068 \\
9 & TGGCG & 0.275 & 0.166 & -0.109 & GCCAG & 0.280 & 0.159 & -0.121 & GCTGG & 0.279 & 0.212 & -0.068 \\
10 & CGGCA & 0.222 & 0.119 & -0.103 & TGGCG & 0.275 & 0.160 & -0.116 & AAAAG & 0.132 & 0.066 & -0.066 \\
\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 & 0.121 & 0.080 & ACCCC & 0.040 & 0.154 & 0.114 & CAAAT & 0.105 & 0.159 & 0.054 \\
2 & CCCCG & 0.055 & 0.135 & 0.080 & GAGAG & 0.046 & 0.153 & 0.107 & GAAGG & 0.094 & 0.131 & 0.038 \\
3 & GAGAG & 0.046 & 0.123 & 0.077 & CCCCG & 0.055 & 0.146 & 0.091 & CTCGT & 0.042 & 0.077 & 0.035 \\
4 & CCCCC & 0.033 & 0.110 & 0.077 & AGAGA & 0.071 & 0.158 & 0.087 & CCCAA & 0.047 & 0.081 & 0.034 \\
5 & CTCCC & 0.040 & 0.111 & 0.071 & CCCCA & 0.064 & 0.142 & 0.078 & AGGCA & 0.093 & 0.126 & 0.032 \\
6 & CCCCA & 0.064 & 0.133 & 0.070 & CTCTC & 0.046 & 0.117 & 0.071 & CTAGA & 0.003 & 0.034 & 0.031 \\
7 & TCCCC & 0.056 & 0.119 & 0.064 & TCCCC & 0.056 & 0.126 & 0.071 & TCTAG & 0.003 & 0.034 & 0.031 \\
8 & TATCT & 0.085 & 0.148 & 0.064 & CTGAG & 0.050 & 0.118 & 0.068 & GGGGT & 0.039 & 0.070 & 0.030 \\
9 & CCCAA & 0.047 & 0.109 & 0.062 & CTAGC & 0.008 & 0.075 & 0.067 & TAGAA & 0.039 & 0.068 & 0.030 \\
10 & CGGGG & 0.054 & 0.116 & 0.061 & CCCCT & 0.039 & 0.104 & 0.065 & TTAGA & 0.026 & 0.055 & 0.029 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/Escherichia_coli/Escherichia_coli_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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/JOGrady_MARC1b_run1/graphs/all_Template_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/all_Complement_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 & 8.92 & 9.14 & 4.76 & 0.00 & 9.15 & 8.60 & 4.98 & 0.00 & 8.63 & 8.37 & 4.11\\
 & C & 8.58 & 0.00 & 9.23 & 9.79 & 9.22 & 0.00 & 8.76 & 9.62 & 9.38 & 0.00 & 10.91 & 9.17\\
 & G & 9.33 & 9.19 & 0.00 & 8.23 & 8.88 & 8.89 & 0.00 & 8.84 & 8.91 & 11.03 & 0.00 & 8.79\\
 & T & 5.07 & 9.16 & 8.59 & 0.00 & 5.24 & 8.77 & 9.04 & 0.00 & 4.19 & 8.12 & 8.39 & 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 (3.21\%) & TTC (3.46\%) & AAA (4.00\%) & TGC (2.71\%) & GGC (2.85\%) & AAA (4.04\%) & GCA (3.13\%) & TCA (2.63\%) & GCA (3.74\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & GCA (2.81\%) & TGC (3.05\%) & TTC (3.72\%) & GCA (2.71\%) & AAA (2.84\%) & GCA (3.52\%) & TTC (2.83\%) & GGC (2.56\%) & AAA (3.70\%)\\
3 & AAA (2.74\%) & GCA (2.85\%) & GCA (3.27\%) & AAA (2.63\%) & TGC (2.75\%) & GAA (3.30\%) & TCA (2.67\%) & AAA (2.54\%) & GAA (3.29\%)\\
4 & TGC (2.67\%) & AAA (2.72\%) & GAA (2.96\%) & TTC (2.61\%) & GCA (2.67\%) & TTC (3.01\%) & ATC (2.55\%) & TGC (2.54\%) & TTC (2.91\%)\\
5 & ATC (2.58\%) & GCC (2.46\%) & TTT (2.67\%) & CAG (2.53\%) & TTC (2.54\%) & TTT (2.70\%) & AAA (2.54\%) & GCA (2.51\%) & TTT (2.78\%)\\
6 & TCA (2.43\%) & TCA (2.45\%) & TGC (2.58\%) & GGC (2.49\%) & GAA (2.40\%) & TCA (2.41\%) & TGC (2.44\%) & TTC (2.41\%) & GCC (2.41\%)\\
7 & GGC (2.27\%) & GGC (2.28\%) & AAT (2.31\%) & GAA (2.31\%) & TCA (2.35\%) & TGC (2.38\%) & GAA (2.35\%) & GCG (2.37\%) & TCA (2.39\%)\\
8 & GCC (2.27\%) & ATC (2.24\%) & TCA (2.26\%) & ATC (2.29\%) & CAG (2.34\%) & ATC (2.29\%) & CAG (2.24\%) & CAG (2.25\%) & ATC (2.30\%)\\
9 & GAA (2.20\%) & AAC (2.19\%) & GCC (2.21\%) & TCA (2.26\%) & GCC (2.32\%) & GCC (2.13\%) & GCG (2.23\%) & CGC (2.18\%) & GTT (2.29\%)\\
10 & TTT (2.18\%) & GAA (2.12\%) & ATC (2.14\%) & GCC (2.14\%) & AGC (2.14\%) & GGC (2.07\%) & CGC (2.20\%) & ATC (2.15\%) & AAT (2.25\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_2D_top_k3.png} \\
\cline{1-10}
-10 & CTC (0.98\%) & GGG (0.93\%) & GGT (0.95\%) & ACT (1.05\%) & ACT (0.95\%) & CTC (0.96\%) & CTC (1.04\%) & GTA (1.02\%) & ACT (0.92\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & AGT (0.98\%) & CCT (0.91\%) & AGA (0.89\%) & AGT (0.98\%) & CCC (0.94\%) & CTT (0.94\%) & CTT (1.04\%) & ACT (0.95\%) & CCT (0.92\%)\\
-8 & CCC (0.92\%) & AGT (0.91\%) & GGG (0.88\%) & CTC (0.95\%) & CGA (0.93\%) & AGT (0.87\%) & GAG (0.92\%) & CGA (0.90\%) & TGA (0.82\%)\\
-7 & AGA (0.89\%) & CTT (0.86\%) & TGT (0.85\%) & GAG (0.89\%) & GGA (0.92\%) & AGG (0.84\%) & AGA (0.84\%) & CTT (0.90\%) & CTT (0.81\%)\\
-6 & GGA (0.86\%) & GAG (0.82\%) & CTT (0.82\%) & GGA (0.89\%) & CTC (0.91\%) & GGG (0.82\%) & AGG (0.82\%) & CCC (0.89\%) & GAG (0.78\%)\\
-5 & GAG (0.74\%) & CGA (0.78\%) & AGG (0.80\%) & CCC (0.87\%) & CCT (0.88\%) & CCT (0.82\%) & GGA (0.79\%) & AGA (0.83\%) & CGA (0.72\%)\\
-4 & GGG (0.68\%) & AGA (0.69\%) & AGT (0.80\%) & AGG (0.71\%) & GAG (0.84\%) & ACT (0.72\%) & CCC (0.79\%) & CCT (0.81\%) & AGA (0.57\%)\\
-3 & AGG (0.68\%) & GGA (0.62\%) & GAG (0.63\%) & GGG (0.61\%) & GGG (0.80\%) & GAG (0.66\%) & GGG (0.73\%) & GGA (0.73\%) & GGA (0.52\%)\\
-2 & CTA (0.47\%) & TAG (0.54\%) & TAG (0.39\%) & CTA (0.56\%) & CTA (0.55\%) & CTA (0.46\%) & CTA (0.59\%) & CTA (0.71\%) & TAG (0.49\%)\\
-1 & TAG (0.40\%) & CTA (0.52\%) & CTA (0.34\%) & TAG (0.47\%) & TAG (0.53\%) & TAG (0.38\%) & TAG (0.49\%) & TAG (0.66\%) & CTA (0.42\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 (1.03\%) & TTTC (1.11\%) & AAAA (1.26\%) & CAGC (1.00\%) & CAGC (1.05\%) & AAAA (1.10\%) & ATCA (0.94\%) & TGGC (0.92\%) & GGCA (1.13\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & GAAA (0.89\%) & TGCC (0.97\%) & TTTC (1.26\%) & ATCA (0.88\%) & TGGC (1.03\%) & CAAA (1.02\%) & GGCA (0.87\%) & CAGC (0.91\%) & GAAA (0.98\%)\\
3 & ATCA (0.87\%) & CAGC (0.92\%) & GAAA (1.17\%) & TGGC (0.88\%) & CGGC (0.99\%) & GAAA (1.01\%) & CAGC (0.86\%) & TTCA (0.90\%) & TGAA (0.96\%)\\
4 & CAGC (0.87\%) & TTCA (0.91\%) & GGCA (0.91\%) & CTGC (0.86\%) & CTGC (0.89\%) & TGAA (0.94\%) & GCCA (0.81\%) & ATCA (0.85\%) & AAAA (0.96\%)\\
5 & AAAA (0.84\%) & TTGC (0.90\%) & GTTC (0.91\%) & CGGC (0.84\%) & ATCA (0.85\%) & ATCA (0.94\%) & TTCA (0.79\%) & CGGC (0.79\%) & TGCA (0.91\%)\\
6 & TTCA (0.82\%) & TGGC (0.88\%) & GCAA (0.89\%) & CCAG (0.82\%) & TTGC (0.82\%) & AGAA (0.92\%) & AACA (0.77\%) & CTGC (0.76\%) & GGAA (0.91\%)\\
7 & TGCC (0.81\%) & CTGC (0.88\%) & TTTT (0.88\%) & CAAA (0.75\%) & CAAA (0.80\%) & AGCA (0.91\%) & CGCA (0.77\%) & CAAA (0.73\%) & AGCA (0.86\%)\\
8 & TGGC (0.81\%) & TTCC (0.84\%) & GGAA (0.87\%) & TTGC (0.75\%) & CTGG (0.77\%) & GGCA (0.91\%) & TTTC (0.74\%) & TGCC (0.73\%) & CAAA (0.85\%)\\
9 & CTTC (0.78\%) & GAAA (0.83\%) & CAAA (0.85\%) & AGCA (0.71\%) & TTCA (0.77\%) & TAAA (0.86\%) & TGAA (0.73\%) & CGCC (0.72\%) & CGCC (0.85\%)\\
10 & GGCA (0.77\%) & AAAA (0.81\%) & TGCC (0.84\%) & AAAA (0.71\%) & CCAG (0.77\%) & TGCA (0.83\%) & CTTC (0.73\%) & GCCA (0.72\%) & TGCC (0.84\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_2D_top_k4.png} \\
\cline{1-10}
-10 & GAGG (0.12\%) & GGAC (0.13\%) & TTAG (0.11\%) & CTAT (0.13\%) & CGAG (0.13\%) & GTAG (0.11\%) & TATA (0.14\%) & CCCC (0.15\%) & TCGA (0.11\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & AGGG (0.12\%) & CTAT (0.13\%) & ACTA (0.10\%) & AGGG (0.12\%) & CCTC (0.12\%) & GGAC (0.10\%) & GTGT (0.14\%) & CTAT (0.15\%) & GGGA (0.11\%)\\
-8 & CTAA (0.11\%) & TCTA (0.12\%) & CGAG (0.10\%) & GAGG (0.11\%) & GTGT (0.12\%) & ACCT (0.10\%) & CCCT (0.13\%) & GAGA (0.15\%) & ACTA (0.11\%)\\
-7 & GGAC (0.11\%) & TAGT (0.12\%) & TAGT (0.09\%) & GGAC (0.10\%) & CTAA (0.12\%) & ACTA (0.10\%) & CTAT (0.13\%) & ACCT (0.14\%) & TCTA (0.11\%)\\
-6 & TCTA (0.11\%) & CGGA (0.10\%) & GGAC (0.09\%) & TAGA (0.10\%) & ACCT (0.11\%) & CTAT (0.10\%) & TCTA (0.13\%) & CTAA (0.13\%) & CTAT (0.10\%)\\
-5 & TTAG (0.10\%) & CTAA (0.10\%) & TAGA (0.07\%) & CTAA (0.10\%) & TAGA (0.10\%) & CGAG (0.09\%) & CTAA (0.12\%) & CCCT (0.10\%) & CGGA (0.09\%)\\
-4 & TAGA (0.07\%) & TAGG (0.07\%) & TCTA (0.07\%) & CCCT (0.10\%) & CCCT (0.08\%) & CCCT (0.06\%) & TAGA (0.08\%) & TAGG (0.09\%) & TAGG (0.07\%)\\
-3 & CCTA (0.06\%) & CCTA (0.06\%) & TAGG (0.06\%) & CCTA (0.07\%) & TAGG (0.07\%) & CCTA (0.06\%) & CCTA (0.07\%) & TAGA (0.09\%) & CCTA (0.05\%)\\
-2 & TAGG (0.04\%) & TAGA (0.05\%) & CCTA (0.04\%) & TAGG (0.05\%) & CCTA (0.06\%) & TAGG (0.06\%) & TAGG (0.05\%) & CCTA (0.09\%) & TAGA (0.05\%)\\
-1 & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.01\%) & CTAG (0.02\%) & CTAG (0.02\%) & CTAG (0.01\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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 & CAGCA (0.37\%) & CAGCA (0.39\%) & CAGCA (0.43\%) & CAGCA (0.41\%) & CAGCA (0.43\%) & CAGCA (0.53\%) & CAGCA (0.39\%) & CTGGC (0.37\%) & CAGCA (0.47\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & TTATC (0.34\%) & CTGGC (0.36\%) & GAAAA (0.39\%) & CCAGC (0.35\%) & CTGGC (0.39\%) & CGGCA (0.35\%) & CGCCA (0.33\%) & CAGCA (0.33\%) & CGGCA (0.41\%)\\
3 & CTGGC (0.33\%) & TTGCC (0.34\%) & CAAAA (0.35\%) & CTGGC (0.33\%) & CCAGC (0.33\%) & ATAAA (0.35\%) & CGGCA (0.33\%) & CATCA (0.31\%) & TGGCA (0.38\%)\\
4 & CGCCA (0.30\%) & GCTGC (0.32\%) & TGTTC (0.33\%) & CATCA (0.32\%) & GCGGC (0.33\%) & CAGAA (0.35\%) & CTGGC (0.30\%) & GCGGC (0.29\%) & GAAAA (0.34\%)\\
5 & GCAGC (0.29\%) & TTTGC (0.31\%) & CGTTC (0.32\%) & GCTGC (0.31\%) & CATCA (0.33\%) & CATCA (0.34\%) & CCAGC (0.29\%) & CCAGC (0.29\%) & GCAAA (0.30\%)\\
6 & ATTTC (0.29\%) & CGCCA (0.31\%) & TGGCA (0.32\%) & GCGGC (0.30\%) & TCAGC (0.31\%) & AAGAA (0.34\%) & TGGCA (0.29\%) & CGCCA (0.29\%) & CGCCA (0.29\%)\\
7 & CATCA (0.28\%) & GCAGC (0.31\%) & GCAAA (0.32\%) & TTATC (0.28\%) & AATCA (0.31\%) & GAAAA (0.33\%) & CATCA (0.29\%) & TTTCA (0.28\%) & ATTTT (0.28\%)\\
8 & TCTTC (0.28\%) & TTTCA (0.30\%) & TCTTC (0.32\%) & CGGCA (0.28\%) & GCTGC (0.30\%) & AATCA (0.33\%) & GCCAG (0.27\%) & GCCAG (0.28\%) & TGAAA (0.28\%)\\
9 & CCAGC (0.28\%) & CATCA (0.30\%) & AGAAA (0.31\%) & AATCA (0.28\%) & ATAAA (0.30\%) & TTATC (0.32\%) & GCAAA (0.26\%) & ATAAA (0.26\%) & TTGCC (0.28\%)\\
10 & TGGCG (0.28\%) & ATTTC (0.29\%) & CTGGC (0.31\%) & GCAGC (0.27\%) & TTTGC (0.28\%) & AGAAA (0.32\%) & GCGCA (0.25\%) & TGGCG (0.26\%) & AAGAA (0.28\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_2D_top_k5.png} \\
\cline{1-10}
-10 & GGACC (0.01\%) & GGACC (0.01\%) & CCCTA (0.01\%) & CTAGC (0.01\%) & CCCCT (0.01\%) & CCCTA (0.01\%) & TAGGA (0.01\%) & TCCTA (0.01\%) & TCCTA (0.01\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & CCCTA (0.01\%) & TAGGA (0.01\%) & ACCTA (0.01\%) & ACCTA (0.01\%) & CCCTA (0.01\%) & CTAGC (0.01\%) & CCCTA (0.01\%) & GCTAG (0.01\%) & CCCTA (0.01\%)\\
-8 & CTAGC (0.00\%) & GCTAG (0.00\%) & ACTAG (0.00\%) & CCCTA (0.01\%) & CTAGC (0.01\%) & ACCTA (0.01\%) & GCTAG (0.01\%) & TAGGA (0.01\%) & GCTAG (0.01\%)\\
-7 & CTAGT (0.00\%) & CTAGC (0.00\%) & GCTAG (0.00\%) & GCTAG (0.01\%) & GCTAG (0.01\%) & GCTAG (0.00\%) & CTAGC (0.00\%) & ACTAG (0.01\%) & CTAGC (0.01\%)\\
-6 & CCTAG (0.00\%) & ACTAG (0.00\%) & CTAGC (0.00\%) & CTAGT (0.00\%) & CTAGT (0.00\%) & CTAGA (0.00\%) & ACTAG (0.00\%) & CTAGC (0.01\%) & CTAGT (0.00\%)\\
-5 & GCTAG (0.00\%) & CTAGT (0.00\%) & CTAGT (0.00\%) & ACTAG (0.00\%) & CTAGA (0.00\%) & CTAGT (0.00\%) & CTAGT (0.00\%) & CTAGT (0.00\%) & ACTAG (0.00\%)\\
-4 & ACTAG (0.00\%) & TCTAG (0.00\%) & CTAGA (0.00\%) & TCTAG (0.00\%) & ACTAG (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & TCTAG (0.00\%) & CTAGG (0.00\%)\\
-3 & TCTAG (0.00\%) & CTAGG (0.00\%) & CTAGG (0.00\%) & CTAGA (0.00\%) & CTAGG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%) & CTAGA (0.00\%) & TCTAG (0.00\%)\\
-2 & CTAGG (0.00\%) & CTAGA (0.00\%) & CCTAG (0.00\%) & CCTAG (0.00\%) & CCTAG (0.00\%) & ACTAG (0.00\%) & CTAGA (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%)\\
-1 & CTAGA (0.00\%) & CCTAG (0.00\%) & TCTAG (0.00\%) & CTAGG (0.00\%) & TCTAG (0.00\%) & CCTAG (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & CTAGA (0.00\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_substitution_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_insertion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_run1/graphs/motifs/logo_deletion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/JOGrady_MARC1b_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}
