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====Alignment Positions==== {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> |- style="font-size:12pt;font-weight:bold" align="center" |style="background-color:#92CDDC" width="150" height="30" | Alignment Position (on Reference) |style="background-color:#92CDDC" width="100" | Counts |style="background-color:#92CDDC" width="120" | Percent of Aligned Reads |style="background-color:#95B3D7" width="150" | Alignment Position (on Reference) |style="background-color:#95B3D7" width="100" | Counts |style="background-color:#95B3D7" width="120" | Percent of Aligned Reads |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 1 | align="center" | 828175 | align="center" | 78.6 |style="font-weight:bold" align="center" | 15 | align="center" | 2638 | align="center" | 0.3 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 2 | align="center" | 36858 | align="center" | 3.5 |style="font-weight:bold" align="center" | 16 | align="center" | 2640 | align="center" | 0.3 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 3 | align="center" | 24997 | align="center" | 2.4 |style="font-weight:bold" align="center" | 17 | align="center" | 2867 | align="center" | 0.3 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 4 | align="center" | 21234 | align="center" | 2.0 |style="font-weight:bold" align="center" | 18 | align="center" | 984 | align="center" | 0.1 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 5 | align="center" | 24639 | align="center" | 2.3 |style="font-weight:bold" align="center" | 19 | align="center" | 540 | align="center" | 0.1 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 6 | align="center" | 37771 | align="center" | 3.6 |style="font-weight:bold" align="center" | 20 | align="center" | 1147 | align="center" | 0.1 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 7 | align="center" | 9018 | align="center" | 0.9 |style="font-weight:bold" align="center" | 21 | align="center" | 1641 | align="center" | 0.2 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 8 | align="center" | 14488 | align="center" | 1.4 |style="font-weight:bold" align="center" | 22 | align="center" | 1273 | align="center" | 0.1 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 9 | align="center" | 2144 | align="center" | 0.2 |style="font-weight:bold" align="center" | 23 | align="center" | 851 | align="center" | 0.1 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 10 | align="center" | 11316 | align="center" | 1.1 |style="font-weight:bold" align="center" | 24 | align="center" | 469 | align="center" | 0.045 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 11 | align="center" | 12873 | align="center" | 1.2 |style="font-weight:bold" align="center" | 25 | align="center" | 151 | align="center" | 0.014 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 12 | align="center" | 2013 | align="center" | 0.2 |style="font-weight:bold" align="center" | 26 | align="center" | 130 | align="center" | 0.012 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 13 | align="center" | 6004 | align="center" | 0.6 |style="font-weight:bold" align="center" | 27 | align="center" | 83 | align="center" | 0.008 |- style="background-color:#BFBFBF;font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 14 | align="center" | 6274 | align="center" | 0.6 |style="font-weight:bold" align="center" | 28 | align="center" | 16 | align="center" | 0.002 |- style="font-size:12pt" align="center" valign="bottom" |style="font-weight:bold" align="center" height="15" | 15 | align="center" | 2638 | align="center" | 0.3 |style="font-weight:bold" align="center" | 29 | align="center" | 6 | align="center" | 0.001 |} Once again, the reads all align to the first 30bp (to start). So let's look at them more closely. The following are the reads aligned to position 1 of the fasta reference (completed amplicon from PCR). [[Image:Miseq20161110-ind31-pos1align-sam.png|1000px]] Now let's look at the bp28 aligned reads again. [[Image:Miseq20161110-ind31-pos28align-sam-highlight.png|1000px]] Aaaaaand we can see that again, many of the reads contain only the AmpF signal, but a few of the reads (designated by the CIGAR string with matching bases at the beginning, highlighted) are interesting. In the next section I will cover the composition of those sequences.
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