\documentclass[a4paper,11pt,oneside]{article}
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\begin{document}
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\section*{\large{NanoOK report for MARC\_1b\_042915}}
\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 & 29550  \\
Complement & 0 & 14966  \\
2D & 0 & 5960  \\
\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 & 29550 & 117943730 & 3991.33 & 295420 & 5 & 5854 & 7094 & 2584 & 18650 \\
Complement & 14966 & 58851294 & 3932.33 & 41615 & 15 & 5425 & 3979 & 2515 & 10088 \\
2D & 5960 & 28634223 & 4804.40 & 76264 & 138 & 6109 & 1765 & 3140 & 4332 \\
\end{tabular}
}
\end{table}
\vspace{-10mm}
\begin{figure}[H]
\centering
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/all_Template_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/all_Complement_lengths.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 & 29550 & \\
Number of reads with alignments & 13684 & (46.31\%) \\
Number of reads without alignments & 15866 & (53.69\%) \\
\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 & 1133 & 3.83 & 2973.57 & 3212602 & 902.42 & 62 \\
Escherichia coli & 4641652 & 12551 & 42.47 & 5383.80 & 61822318 & 13.32 & 79 \\
\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 & 14966 & \\
Number of reads with alignments & 7866 & (52.56\%) \\
Number of reads without alignments & 7100 & (47.44\%) \\
\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 & 640 & 4.28 & 2751.20 & 1510945 & 424.42 & 46 \\
Escherichia coli & 4641652 & 7226 & 48.28 & 4911.21 & 31607063 & 6.81 & 68 \\
\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 & 5960 & \\
Number of reads with alignments & 4938 & (82.85\%) \\
Number of reads without alignments & 1022 & (17.15\%) \\
\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 & 610 & 10.23 & 3094.86 & 1916874 & 538.45 & 129 \\
Escherichia coli & 4641652 & 4328 & 72.62 & 5484.88 & 24276937 & 5.23 & 207 \\
\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) & 62.86\% & 55.74\% & 75.17\% \\
Aligned base identity (excluding indels) & 78.88\% & 80.22\% & 86.00\% \\
Identical bases per 100 aligned bases (including indels) & 65.92\% & 64.96\% & 74.03\% \\
Inserted bases per 100 aligned bases (including indels) & 4.88\% & 3.73\% & 4.34\% \\
Deleted bases per 100 aligned bases (including indels) & 11.55\% & 15.29\% & 9.58\% \\
Substitutions per 100 aligned bases (including indels) & 17.65\% & 16.02\% & 12.05\% \\
Mean insertion size & 1.55 & 1.48 & 1.48 \\
Mean deletion size & 1.69 & 1.89 & 1.66 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 & 0.116 & -0.643 & TTTTT & 0.759 & 0.070 & -0.689 & TTTTT & 0.759 & 0.040 & -0.719 \\
2 & AAAAA & 0.478 & 0.081 & -0.397 & AAAAA & 0.478 & 0.037 & -0.440 & AAAAA & 0.478 & 0.047 & -0.431 \\
3 & TGATG & 0.393 & 0.127 & -0.266 & AAAAC & 0.337 & 0.107 & -0.230 & TGATG & 0.393 & 0.154 & -0.239 \\
4 & AAAAC & 0.337 & 0.115 & -0.222 & GATGT & 0.309 & 0.107 & -0.202 & AAAAC & 0.337 & 0.137 & -0.200 \\
5 & GATGT & 0.309 & 0.094 & -0.215 & TGATG & 0.393 & 0.206 & -0.187 & GATGT & 0.309 & 0.121 & -0.188 \\
6 & CTGAT & 0.309 & 0.102 & -0.207 & GCAAT & 0.309 & 0.126 & -0.184 & CTGAT & 0.309 & 0.139 & -0.171 \\
7 & GCAAT & 0.309 & 0.120 & -0.189 & AATAT & 0.309 & 0.127 & -0.182 & GCAAT & 0.309 & 0.147 & -0.162 \\
8 & AATAT & 0.309 & 0.122 & -0.187 & TTATC & 0.309 & 0.128 & -0.181 & TTATC & 0.309 & 0.147 & -0.162 \\
9 & TAATA & 0.281 & 0.106 & -0.175 & AACAA & 0.281 & 0.111 & -0.170 & CTTTT & 0.253 & 0.093 & -0.160 \\
10 & GCTGA & 0.281 & 0.107 & -0.174 & TGAAG & 0.253 & 0.085 & -0.168 & TGATT & 0.309 & 0.159 & -0.150 \\
\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 & 0.161 & 0.133 & CTTTG & 0.028 & 0.158 & 0.130 & ATCTA & 0.000 & 0.105 & 0.105 \\
2 & ATCTA & 0.000 & 0.130 & 0.130 & TACTT & 0.000 & 0.126 & 0.126 & GCATC & 0.084 & 0.188 & 0.104 \\
3 & TACTT & 0.000 & 0.122 & 0.122 & CTTAC & 0.000 & 0.123 & 0.123 & TCAGC & 0.028 & 0.132 & 0.103 \\
4 & GCTCC & 0.000 & 0.116 & 0.116 & GGAAT & 0.112 & 0.234 & 0.122 & CAGCA & 0.056 & 0.156 & 0.100 \\
5 & CATCT & 0.000 & 0.112 & 0.112 & TACAT & 0.028 & 0.150 & 0.122 & TCTAC & 0.000 & 0.099 & 0.099 \\
6 & CCCCA & 0.000 & 0.112 & 0.112 & GGCTT & 0.056 & 0.176 & 0.119 & CCCGC & 0.000 & 0.097 & 0.097 \\
7 & ACCCC & 0.000 & 0.108 & 0.108 & TGCGA & 0.028 & 0.146 & 0.118 & TACAT & 0.028 & 0.124 & 0.096 \\
8 & TCTAC & 0.000 & 0.108 & 0.108 & GAGGA & 0.000 & 0.114 & 0.114 & CTTTG & 0.028 & 0.124 & 0.096 \\
9 & TACAT & 0.028 & 0.135 & 0.107 & ACCCC & 0.000 & 0.113 & 0.113 & CATCT & 0.000 & 0.093 & 0.093 \\
10 & ACTCT & 0.000 & 0.101 & 0.101 & TGCTT & 0.084 & 0.197 & 0.113 & TACGC & 0.000 & 0.091 & 0.091 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Control_sequence/Control_sequence_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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) & 60.08\% & 57.69\% & 76.65\% \\
Aligned base identity (excluding indels) & 79.01\% & 80.11\% & 86.55\% \\
Identical bases per 100 aligned bases (including indels) & 65.66\% & 64.78\% & 74.95\% \\
Inserted bases per 100 aligned bases (including indels) & 4.90\% & 3.94\% & 4.65\% \\
Deleted bases per 100 aligned bases (including indels) & 11.99\% & 15.19\% & 8.76\% \\
Substitutions per 100 aligned bases (including indels) & 17.45\% & 16.09\% & 11.65\% \\
Mean insertion size & 1.56 & 1.50 & 1.53 \\
Mean deletion size & 1.73 & 1.89 & 1.66 \\
\end{tabular}
}
\end{table}
\vspace{-5mm}
\begin{figure}[H]
\centering
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_insertions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_insertions.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_deletions.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_hist.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_length_vs_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_length_vs_identity_scatter.png} \\
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_read_fraction_vs_alignment_identity_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_percent_aligned_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_cumulative_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_best_perfect_kmers.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_longest_perfect_vs_length_scatter.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_2D_coverage.png} \\
\includegraphics[height=2cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 & 0.058 & -0.190 & AAAAA & 0.247 & 0.036 & -0.211 & TTTTT & 0.251 & 0.033 & -0.218 \\
2 & TTTTT & 0.251 & 0.075 & -0.176 & CGCCA & 0.288 & 0.084 & -0.204 & AAAAA & 0.247 & 0.038 & -0.209 \\
3 & CGCTG & 0.259 & 0.083 & -0.176 & TTTTT & 0.251 & 0.051 & -0.200 & CGCTG & 0.259 & 0.155 & -0.104 \\
4 & GCTGG & 0.279 & 0.125 & -0.155 & CTGGC & 0.278 & 0.136 & -0.142 & GCTGG & 0.279 & 0.176 & -0.104 \\
5 & CGCCA & 0.288 & 0.140 & -0.148 & TGGCG & 0.275 & 0.135 & -0.140 & CGCCA & 0.288 & 0.185 & -0.103 \\
6 & CTGGC & 0.278 & 0.147 & -0.131 & CGCTG & 0.259 & 0.122 & -0.137 & TGGCG & 0.275 & 0.178 & -0.097 \\
7 & TGGCG & 0.275 & 0.159 & -0.116 & CGCGC & 0.201 & 0.067 & -0.135 & GCCAG & 0.280 & 0.187 & -0.093 \\
8 & GCCAG & 0.280 & 0.164 & -0.116 & CCAGC & 0.289 & 0.156 & -0.133 & AAAAT & 0.195 & 0.103 & -0.092 \\
9 & CCAGC & 0.289 & 0.177 & -0.112 & GCGCA & 0.202 & 0.073 & -0.129 & CCAGC & 0.289 & 0.200 & -0.088 \\
10 & CGCGC & 0.201 & 0.096 & -0.105 & CAGCA & 0.261 & 0.133 & -0.129 & TGCGC & 0.201 & 0.115 & -0.086 \\
\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 & 0.137 & 0.097 & ACCCC & 0.040 & 0.136 & 0.095 & CTAGA & 0.003 & 0.070 & 0.067 \\
2 & CCTAG & 0.003 & 0.097 & 0.094 & TAGGA & 0.012 & 0.100 & 0.088 & GGGGT & 0.039 & 0.105 & 0.066 \\
3 & CCCCG & 0.055 & 0.140 & 0.085 & CCTAG & 0.003 & 0.075 & 0.072 & TCTAG & 0.003 & 0.068 & 0.065 \\
4 & ATCTA & 0.033 & 0.117 & 0.084 & TCCTA & 0.013 & 0.084 & 0.071 & GGGTC & 0.040 & 0.103 & 0.063 \\
5 & CCCCA & 0.064 & 0.146 & 0.083 & ATTTA & 0.112 & 0.182 & 0.070 & CTCGT & 0.042 & 0.104 & 0.061 \\
6 & TAGGA & 0.012 & 0.094 & 0.082 & CCTAT & 0.028 & 0.098 & 0.070 & CCCAA & 0.047 & 0.106 & 0.059 \\
7 & GGATT & 0.098 & 0.180 & 0.082 & TACCC & 0.073 & 0.142 & 0.069 & TCTAA & 0.025 & 0.082 & 0.057 \\
8 & CCCCC & 0.033 & 0.114 & 0.081 & TACCT & 0.062 & 0.130 & 0.068 & CCTAG & 0.003 & 0.060 & 0.057 \\
9 & CTCCC & 0.040 & 0.120 & 0.080 & TGCTT & 0.099 & 0.167 & 0.068 & ATCTA & 0.033 & 0.090 & 0.057 \\
10 & TACCC & 0.073 & 0.149 & 0.076 & GGAAT & 0.089 & 0.157 & 0.067 & TAGAT & 0.035 & 0.091 & 0.057 \\
\cline{1-13}
\end{tabular}
}
\end{table}
\vspace{-8mm}
\begin{figure}[H]
\centering
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_kmer_scatter.png} 
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_kmer_scatter.png} \\
\includegraphics[height=8cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Template_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/Escherichia_coli/Escherichia_coli_Complement_GC_hist.png}
\includegraphics[height=3.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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/MARC_1b_042915/graphs/all_Template_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/all_Complement_21mers.png}
\includegraphics[width=.3\linewidth]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 & 8.96 & 8.87 & 5.06 & 0.00 & 9.04 & 8.56 & 5.28 & 0.00 & 9.54 & 8.71 & 4.66\\
 & C & 8.59 & 0.00 & 8.88 & 9.91 & 9.03 & 0.00 & 8.57 & 9.77 & 8.42 & 0.00 & 10.09 & 8.72\\
 & G & 9.61 & 8.94 & 0.00 & 8.29 & 9.07 & 8.72 & 0.00 & 8.71 & 8.75 & 10.31 & 0.00 & 8.08\\
 & T & 5.31 & 8.87 & 8.72 & 0.00 & 5.57 & 8.64 & 9.03 & 0.00 & 4.75 & 8.64 & 9.33 & 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 (3.24\%) & TTC (3.24\%) & AAA (4.01\%) & TGC (2.83\%) & AAA (2.89\%) & AAA (3.98\%) & GCA (3.17\%) & AAA (2.74\%) & GCA (3.69\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & AAA (2.80\%) & TGC (3.00\%) & TTC (3.59\%) & GCA (2.81\%) & GGC (2.80\%) & GCA (3.55\%) & AAA (2.82\%) & GGC (2.68\%) & AAA (3.67\%)\\
3 & GCA (2.78\%) & AAA (2.84\%) & GCA (3.26\%) & TTC (2.78\%) & TGC (2.80\%) & GAA (3.26\%) & TTC (2.64\%) & GCA (2.63\%) & GAA (3.00\%)\\
4 & TGC (2.59\%) & GCA (2.73\%) & GAA (2.90\%) & AAA (2.65\%) & GCA (2.72\%) & TTC (3.07\%) & TCA (2.52\%) & TGC (2.61\%) & TTT (2.87\%)\\
5 & ATC (2.56\%) & GCC (2.54\%) & TTT (2.71\%) & CAG (2.49\%) & TTC (2.58\%) & TTT (2.69\%) & GAA (2.39\%) & GAA (2.35\%) & GTT (2.68\%)\\
6 & TCA (2.38\%) & GGC (2.40\%) & TGC (2.60\%) & GAA (2.40\%) & GAA (2.57\%) & TGC (2.47\%) & GCG (2.28\%) & GCG (2.35\%) & TTC (2.64\%)\\
7 & GAA (2.26\%) & TCA (2.28\%) & AAT (2.43\%) & TCA (2.32\%) & CAG (2.36\%) & TCA (2.29\%) & TGC (2.26\%) & TCA (2.30\%) & AAT (2.46\%)\\
8 & TTT (2.24\%) & ATC (2.18\%) & GCC (2.24\%) & GGC (2.30\%) & GCC (2.24\%) & AAT (2.23\%) & ATC (2.24\%) & CAG (2.30\%) & GCC (2.23\%)\\
9 & GCC (2.23\%) & GAA (2.18\%) & CAA (2.15\%) & ATC (2.24\%) & TCA (2.21\%) & CAA (2.16\%) & AAT (2.19\%) & TTC (2.23\%) & TCA (2.14\%)\\
10 & GGC (2.17\%) & AAT (2.15\%) & ATC (2.15\%) & AAT (2.18\%) & AAT (2.18\%) & ATC (2.15\%) & CAG (2.17\%) & GCC (2.22\%) & TGC (2.10\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_top_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_2D_top_k3.png} \\
\cline{1-10}
-10 & AGT (0.96\%) & AGG (0.99\%) & GGT (0.93\%) & AGT (0.98\%) & AGT (0.96\%) & CCC (0.89\%) & TAC (1.03\%) & GTA (1.04\%) & TGA (1.01\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & CTC (0.93\%) & AGT (0.90\%) & GGG (0.89\%) & AGA (0.97\%) & ACT (0.95\%) & AGT (0.89\%) & CTT (1.00\%) & CCC (1.03\%) & CCT (0.99\%)\\
-8 & GGA (0.92\%) & CCT (0.89\%) & AGA (0.87\%) & GGA (0.93\%) & CTT (0.95\%) & CCT (0.86\%) & GGA (0.92\%) & CGA (0.93\%) & ACT (0.95\%)\\
-7 & CCC (0.90\%) & GAG (0.88\%) & AGG (0.86\%) & CTC (0.83\%) & CCC (0.94\%) & AGG (0.85\%) & GAG (0.92\%) & AGA (0.90\%) & GAG (0.90\%)\\
-6 & AGA (0.84\%) & CTT (0.86\%) & TGT (0.84\%) & CCC (0.81\%) & CCT (0.88\%) & CTC (0.84\%) & AGA (0.88\%) & ACT (0.88\%) & CGA (0.82\%)\\
-5 & GAG (0.73\%) & CGA (0.84\%) & CTT (0.79\%) & AGG (0.75\%) & GAG (0.86\%) & ACT (0.79\%) & AGG (0.83\%) & CTT (0.86\%) & CTT (0.80\%)\\
-4 & GGG (0.71\%) & AGA (0.73\%) & AGT (0.77\%) & GAG (0.74\%) & CTC (0.83\%) & GGG (0.76\%) & CCC (0.78\%) & CCT (0.82\%) & AGA (0.72\%)\\
-3 & AGG (0.70\%) & GGA (0.72\%) & GAG (0.63\%) & GGG (0.59\%) & GGG (0.78\%) & GAG (0.61\%) & GGG (0.73\%) & GGA (0.79\%) & GGA (0.68\%)\\
-2 & CTA (0.51\%) & TAG (0.54\%) & TAG (0.40\%) & CTA (0.52\%) & TAG (0.54\%) & TAG (0.40\%) & CTA (0.63\%) & TAG (0.69\%) & TAG (0.52\%)\\
-1 & TAG (0.43\%) & CTA (0.49\%) & CTA (0.36\%) & TAG (0.43\%) & CTA (0.50\%) & CTA (0.39\%) & TAG (0.53\%) & CTA (0.66\%) & CTA (0.43\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_bottom_k3.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 (1.06\%) & TTTC (1.10\%) & TTTC (1.31\%) & CAGC (0.89\%) & TGGC (1.03\%) & AAAA (1.03\%) & GGCA (0.87\%) & TGGC (1.04\%) & GGCA (1.23\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & GAAA (0.89\%) & TGCC (0.97\%) & AAAA (1.29\%) & ATCA (0.86\%) & CAGC (1.00\%) & CAAA (1.03\%) & ATCA (0.87\%) & CAGC (0.92\%) & AAAA (1.02\%)\\
3 & AAAA (0.86\%) & TGGC (0.93\%) & GAAA (1.10\%) & CTGC (0.86\%) & CGGC (0.99\%) & GAAA (0.96\%) & GCCA (0.83\%) & CTGC (0.81\%) & GGAA (0.97\%)\\
4 & TTCA (0.82\%) & TTGC (0.92\%) & GGCA (0.97\%) & TGGC (0.85\%) & CTGC (0.89\%) & GGCA (0.94\%) & AACA (0.82\%) & TTCA (0.80\%) & GAAA (0.97\%)\\
5 & ATCA (0.81\%) & CAGC (0.90\%) & TTTT (0.91\%) & CCAG (0.81\%) & CAAA (0.87\%) & AGCA (0.94\%) & TTTC (0.79\%) & CAAA (0.80\%) & CGTT (0.90\%)\\
6 & TGCC (0.81\%) & CTGC (0.87\%) & GCAA (0.91\%) & TTGC (0.80\%) & TTGC (0.86\%) & TGAA (0.93\%) & CAAA (0.79\%) & CGGC (0.79\%) & TGCA (0.90\%)\\
7 & TGGC (0.80\%) & TTCC (0.87\%) & GGAA (0.88\%) & CAAA (0.78\%) & TTCC (0.82\%) & TTTC (0.93\%) & GAAA (0.79\%) & TGCC (0.77\%) & CAAA (0.88\%)\\
8 & GGCA (0.79\%) & TTCA (0.86\%) & CAAA (0.88\%) & CGGC (0.74\%) & TGCC (0.80\%) & GGAA (0.87\%) & TGGC (0.76\%) & GGAA (0.75\%) & TTTC (0.88\%)\\
9 & TTGC (0.78\%) & AAAA (0.83\%) & AAAT (0.87\%) & TTCA (0.74\%) & CCAG (0.78\%) & ATCA (0.86\%) & TTCA (0.76\%) & CCAG (0.74\%) & TGTT (0.87\%)\\
10 & CAGC (0.77\%) & GAAA (0.81\%) & TGCC (0.86\%) & GGCA (0.74\%) & ATCA (0.77\%) & TAAA (0.85\%) & TGCA (0.76\%) & GGCA (0.73\%) & TTTT (0.82\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_top_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_2D_top_k4.png} \\
\cline{1-10}
-10 & TCTA (0.12\%) & CCCT (0.12\%) & CTAT (0.11\%) & GGGG (0.12\%) & ACCT (0.11\%) & TAGA (0.11\%) & TCTA (0.15\%) & ACTA (0.15\%) & TATA (0.13\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & CTAA (0.12\%) & CTAT (0.12\%) & CGAG (0.10\%) & GTGT (0.11\%) & ACTA (0.11\%) & TCTA (0.10\%) & CCCC (0.14\%) & CGGA (0.15\%) & CCCT (0.11\%)\\
-8 & TTAG (0.11\%) & CGGA (0.12\%) & TAGT (0.09\%) & CGAG (0.11\%) & TAGA (0.11\%) & ACTA (0.10\%) & CTAA (0.14\%) & CTAA (0.14\%) & CGGA (0.11\%)\\
-7 & TAGT (0.11\%) & GGAC (0.11\%) & TAGA (0.09\%) & GGAC (0.10\%) & CTAT (0.11\%) & CTAT (0.10\%) & GGAC (0.14\%) & ACTT (0.14\%) & ACTT (0.11\%)\\
-6 & GAGG (0.10\%) & TAGT (0.11\%) & ACTA (0.09\%) & TAGA (0.10\%) & CTAA (0.11\%) & GGAC (0.09\%) & ACTA (0.14\%) & ACCT (0.13\%) & TCTA (0.11\%)\\
-5 & GGAC (0.09\%) & CTAA (0.10\%) & TCTA (0.08\%) & GAGG (0.10\%) & CCCC (0.10\%) & CGAG (0.09\%) & CCCT (0.13\%) & CCCT (0.11\%) & ACTA (0.10\%)\\
-4 & TAGA (0.07\%) & TAGG (0.08\%) & GGAC (0.08\%) & CCCT (0.10\%) & CCCT (0.09\%) & CCCT (0.07\%) & TAGA (0.10\%) & TAGG (0.10\%) & TAGG (0.08\%)\\
-3 & CCTA (0.07\%) & TAGA (0.06\%) & TAGG (0.07\%) & CCTA (0.06\%) & TAGG (0.07\%) & TAGG (0.06\%) & CCTA (0.09\%) & TAGA (0.10\%) & TAGA (0.07\%)\\
-2 & TAGG (0.05\%) & CCTA (0.05\%) & CCTA (0.05\%) & TAGG (0.06\%) & CCTA (0.06\%) & CCTA (0.05\%) & TAGG (0.06\%) & CCTA (0.08\%) & CCTA (0.06\%)\\
-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/MARC_1b_042915/graphs/motifs/logo_insertion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_bottom_k4.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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 (0.35\%) & CTGGC (0.38\%) & GAAAA (0.43\%) & CAGCA (0.43\%) & CAGCA (0.42\%) & CAGCA (0.54\%) & CAGCA (0.39\%) & CTGGC (0.44\%) & TGGCA (0.47\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Most common}}\\
2 & TTATC (0.33\%) & CAGCA (0.34\%) & CAGCA (0.40\%) & CATCA (0.32\%) & CTGGC (0.41\%) & CGGCA (0.37\%) & CGCCA (0.36\%) & CAGCA (0.32\%) & CAGCA (0.43\%)\\
3 & CTGGC (0.32\%) & TTGCC (0.34\%) & CAAAA (0.35\%) & CCAGC (0.31\%) & CCAGC (0.33\%) & GAAAA (0.35\%) & CTGGC (0.34\%) & GCGGC (0.31\%) & CGGCA (0.41\%)\\
4 & ATTTC (0.31\%) & TTTGC (0.33\%) & TGGCA (0.34\%) & GCTGC (0.31\%) & GCGGC (0.33\%) & CATCA (0.33\%) & TGGCA (0.32\%) & GCCAG (0.30\%) & GAAAA (0.38\%)\\
5 & TGGCG (0.30\%) & GCTGC (0.32\%) & CGTTT (0.32\%) & CTGGC (0.31\%) & GCTGC (0.32\%) & TGGCA (0.32\%) & CGGCA (0.31\%) & TGGCG (0.30\%) & GCGTT (0.36\%)\\
6 & CATCA (0.29\%) & GCAGC (0.31\%) & CTGGC (0.32\%) & GCGGC (0.29\%) & CATCA (0.31\%) & CAGAA (0.32\%) & TGGCG (0.30\%) & GCAGC (0.30\%) & TGGCG (0.32\%)\\
7 & CGCCA (0.29\%) & CGCCA (0.31\%) & CGTTC (0.32\%) & CGGCA (0.29\%) & TTTGC (0.30\%) & ATAAA (0.32\%) & GCAAA (0.29\%) & CCAGC (0.29\%) & GCAAA (0.30\%)\\
8 & CGTTT (0.28\%) & GCCAG (0.31\%) & TGTTC (0.31\%) & AATCA (0.28\%) & GCTGG (0.30\%) & AAGAA (0.32\%) & CATCA (0.28\%) & CGCCA (0.28\%) & CTGCA (0.30\%)\\
9 & TTTCT (0.28\%) & TTTCA (0.29\%) & TTGCC (0.31\%) & TTTGC (0.28\%) & AATCA (0.30\%) & AATCA (0.32\%) & CTGCA (0.26\%) & TGGCA (0.27\%) & AGGAA (0.30\%)\\
10 & GAAAA (0.28\%) & TTTCC (0.29\%) & GCAAA (0.30\%) & GCCAG (0.27\%) & GCAGC (0.30\%) & ACGCA (0.31\%) & GAAAA (0.26\%) & GCTGC (0.27\%) & TGGAA (0.29\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_top_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_2D_top_k5.png} \\
\cline{1-10}
-10 & CTTAG (0.01\%) & GGACC (0.01\%) & CCCTA (0.01\%) & GGGGG (0.01\%) & TAGGG (0.01\%) & TAGGG (0.01\%) & CCCTA (0.01\%) & TAGGA (0.01\%) & CCCTA (0.01\%) & \multirow{10}{*}{\rotatebox[origin=c]{90}{Least common}}\\
-9 & GGACC (0.01\%) & CCCTA (0.01\%) & TAGGT (0.01\%) & CTAGT (0.01\%) & CCCCC (0.01\%) & CCCCC (0.01\%) & GGACC (0.01\%) & TCCTA (0.01\%) & TTAGA (0.01\%)\\
-8 & GCTAG (0.00\%) & GCTAG (0.00\%) & ACTAG (0.00\%) & CCCTA (0.01\%) & CTAGC (0.01\%) & CCCTA (0.01\%) & GCTAG (0.01\%) & GCTAG (0.01\%) & ACTAG (0.01\%)\\
-7 & ACTAG (0.00\%) & CTAGC (0.00\%) & GCTAG (0.00\%) & CTAGC (0.00\%) & ACTAG (0.00\%) & GCTAG (0.00\%) & CTAGC (0.00\%) & CTAGC (0.01\%) & GCTAG (0.00\%)\\
-6 & CTAGT (0.00\%) & ACTAG (0.00\%) & CTAGC (0.00\%) & GCTAG (0.00\%) & GCTAG (0.00\%) & CTAGC (0.00\%) & CCTAG (0.00\%) & ACTAG (0.01\%) & CTAGC (0.00\%)\\
-5 & CTAGG (0.00\%) & CTAGT (0.00\%) & CTAGG (0.00\%) & CTAGA (0.00\%) & CTAGG (0.00\%) & CTAGT (0.00\%) & ACTAG (0.00\%) & CTAGT (0.00\%) & CTAGA (0.00\%)\\
-4 & CCTAG (0.00\%) & CCTAG (0.00\%) & CTAGT (0.00\%) & TCTAG (0.00\%) & CTAGT (0.00\%) & CTAGG (0.00\%) & CTAGA (0.00\%) & CTAGA (0.00\%) & CTAGT (0.00\%)\\
-3 & CTAGC (0.00\%) & TCTAG (0.00\%) & CTAGA (0.00\%) & ACTAG (0.00\%) & CTAGA (0.00\%) & ACTAG (0.00\%) & CTAGT (0.00\%) & CTAGG (0.00\%) & CTAGG (0.00\%)\\
-2 & CTAGA (0.00\%) & CTAGA (0.00\%) & CCTAG (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%) & TCTAG (0.00\%)\\
-1 & TCTAG (0.00\%) & CTAGG (0.00\%) & TCTAG (0.00\%) & CCTAG (0.00\%) & TCTAG (0.00\%) & CTAGA (0.00\%) & CTAGG (0.00\%) & CCTAG (0.00\%) & CCTAG (0.00\%)\\
\cline{1-10}
\rule{0pt}{0.6cm}
  & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Template_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_substitution_Complement_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_insertion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/graphs/motifs/logo_deletion_2D_bottom_k5.png} & \includegraphics[height=0.5cm]{/tgac/workarea/group-si/marc/MARC_1b_042915/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}
