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<h1 class="title toc-ignore">Analysis of coronavirus sequences</h1>
<h4 class="author">Jacques van Helden</h4>
<h4 class="date">2021-02-14</h4>
</div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co">#### General parameters for the analysis ####</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co">## Use (or not) GIDAID sequences</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co">## </span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"><span class="co">## A few genoes were not available in NCBI Genbank at the time of </span></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">## this analysis, and had to be downloaded from GISAID. These sequences</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="co">## can however not be redistributed, they should thus be downloaded </span></a>
<a class="sourceLine" id="cb1-8" data-line-number="8"><span class="co">## manually to reproduce the full trees. Alternatively, useGISAID</span></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">## can be set to FALSE, whcih will reproduce the analysis with almost </span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="co">## all the sequences of the paper.</span></a>
<a class="sourceLine" id="cb1-11" data-line-number="11">useGISAID <-<span class="st"> </span><span class="ot">TRUE</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">## Sequence collection</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="co">## Supported: </span></a>
<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="co">## collection <- "around-CoV-2" # ~20 genomes</span></a>
<a class="sourceLine" id="cb1-16" data-line-number="16"><span class="co">## collection <- "selected" # ~60 genomes</span></a>
<a class="sourceLine" id="cb1-17" data-line-number="17"><span class="co">## collection <- "all" # ~60 genomes</span></a>
<a class="sourceLine" id="cb1-18" data-line-number="18">collections <-<span class="st"> </span><span class="kw">c</span>(<span class="st">"around-CoV-2"</span>, <span class="st">"selected"</span>, <span class="st">"all"</span>)</a>
<a class="sourceLine" id="cb1-19" data-line-number="19">collection <-<span class="st"> "around-CoV-2"</span> <span class="co"># ~20 genomes</span></a>
<a class="sourceLine" id="cb1-20" data-line-number="20"></a>
<a class="sourceLine" id="cb1-21" data-line-number="21"></a>
<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co">#### Define directories and files ####</span></a>
<a class="sourceLine" id="cb1-23" data-line-number="23">dir <-<span class="st"> </span><span class="kw">list</span>(<span class="dt">main =</span> <span class="st">'..'</span>)</a>
<a class="sourceLine" id="cb1-24" data-line-number="24">dir<span class="op">$</span>R <-<span class="st"> </span><span class="kw">file.path</span>(dir<span class="op">$</span>main, <span class="st">"scripts/R"</span>)</a>
<a class="sourceLine" id="cb1-25" data-line-number="25"></a>
<a class="sourceLine" id="cb1-26" data-line-number="26"><span class="co">#### Create output directory for sequences ####</span></a>
<a class="sourceLine" id="cb1-27" data-line-number="27">dir<span class="op">$</span>outseq <-<span class="st"> </span><span class="kw">file.path</span>(</a>
<a class="sourceLine" id="cb1-28" data-line-number="28"> dir<span class="op">$</span>main, <span class="st">"results"</span>, <span class="st">"S-gene"</span>, <span class="st">"Nto1_alignments"</span>)</a>
<a class="sourceLine" id="cb1-29" data-line-number="29"><span class="kw">dir.create</span>(dir<span class="op">$</span>outseq, <span class="dt">showWarnings =</span> <span class="ot">FALSE</span>, <span class="dt">recursive =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb1-30" data-line-number="30"></a>
<a class="sourceLine" id="cb1-31" data-line-number="31"><span class="co">## Instantiate a list for output files</span></a>
<a class="sourceLine" id="cb1-32" data-line-number="32">outfiles <-<span class="st"> </span><span class="kw">vector</span>()</a>
<a class="sourceLine" id="cb1-33" data-line-number="33"></a>
<a class="sourceLine" id="cb1-34" data-line-number="34"><span class="co">## Input files</span></a>
<a class="sourceLine" id="cb1-35" data-line-number="35">infiles <-<span class="st"> </span><span class="kw">list</span>()</a>
<a class="sourceLine" id="cb1-36" data-line-number="36"></a>
<a class="sourceLine" id="cb1-37" data-line-number="37"></a>
<a class="sourceLine" id="cb1-38" data-line-number="38"></a>
<a class="sourceLine" id="cb1-39" data-line-number="39"><span class="co">## Genome dir and files</span></a>
<a class="sourceLine" id="cb1-40" data-line-number="40"><span class="cf">if</span> (useGISAID) {</a>
<a class="sourceLine" id="cb1-41" data-line-number="41"> dir<span class="op">$</span>genomes <-<span class="st"> </span><span class="kw">file.path</span>(dir<span class="op">$</span>main, <span class="st">"data"</span>, <span class="st">"GISAID_genomes"</span>)</a>
<a class="sourceLine" id="cb1-42" data-line-number="42"> infiles<span class="op">$</span>genomes <-<span class="st"> </span><span class="kw">file.path</span>(</a>
<a class="sourceLine" id="cb1-43" data-line-number="43"> dir<span class="op">$</span>genomes, </a>
<a class="sourceLine" id="cb1-44" data-line-number="44"> <span class="kw">paste0</span>(<span class="st">"genomes_"</span>, collection, <span class="st">"-plus-GISAID.fasta"</span>))</a>
<a class="sourceLine" id="cb1-45" data-line-number="45">} <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb1-46" data-line-number="46"> dir<span class="op">$</span>genomes <-<span class="st"> </span><span class="kw">file.path</span>(dir<span class="op">$</span>main, <span class="st">"data"</span>, <span class="st">"virus_genomes"</span>)</a>
<a class="sourceLine" id="cb1-47" data-line-number="47"> infiles<span class="op">$</span>genomes <-<span class="st"> </span><span class="kw">file.path</span>(</a>
<a class="sourceLine" id="cb1-48" data-line-number="48"> dir<span class="op">$</span>genomes, </a>
<a class="sourceLine" id="cb1-49" data-line-number="49"> <span class="kw">paste0</span>(<span class="st">"genomes_"</span>, collection,<span class="st">".fasta"</span>))</a>
<a class="sourceLine" id="cb1-50" data-line-number="50">}</a>
<a class="sourceLine" id="cb1-51" data-line-number="51"></a>
<a class="sourceLine" id="cb1-52" data-line-number="52"><span class="co">## Genome sequences</span></a>
<a class="sourceLine" id="cb1-53" data-line-number="53"><span class="cf">if</span> (<span class="op">!</span><span class="kw">file.exists</span>(infiles<span class="op">$</span>genomes)) {</a>
<a class="sourceLine" id="cb1-54" data-line-number="54"> <span class="kw">stop</span>(<span class="st">"Genome sequence file is missing"</span>, <span class="st">"</span><span class="ch">\n</span><span class="st">"</span>, infiles<span class="op">$</span>genomes)</a>
<a class="sourceLine" id="cb1-55" data-line-number="55">}</a>
<a class="sourceLine" id="cb1-56" data-line-number="56"></a>
<a class="sourceLine" id="cb1-57" data-line-number="57"></a>
<a class="sourceLine" id="cb1-58" data-line-number="58"><span class="co">## Output tables</span></a>
<a class="sourceLine" id="cb1-59" data-line-number="59"><span class="co"># di$output <- file.path(dir.main, "")</span></a>
<a class="sourceLine" id="cb1-60" data-line-number="60"><span class="co"># dir$tables <- </span></a>
<a class="sourceLine" id="cb1-61" data-line-number="61"></a>
<a class="sourceLine" id="cb1-62" data-line-number="62"><span class="co">## Load custom functions</span></a>
<a class="sourceLine" id="cb1-63" data-line-number="63"><span class="kw">source</span>(<span class="kw">file.path</span>(dir<span class="op">$</span>R, <span class="st">"align_n_to_one.R"</span>))</a>
<a class="sourceLine" id="cb1-64" data-line-number="64"><span class="kw">source</span>(<span class="kw">file.path</span>(dir<span class="op">$</span>R, <span class="st">"plot_pip_profiles.R"</span>))</a>
<a class="sourceLine" id="cb1-65" data-line-number="65"><span class="kw">source</span>(<span class="kw">file.path</span>(dir<span class="op">$</span>R, <span class="st">"plot_pip_profiles_from_list.R"</span>))</a>
<a class="sourceLine" id="cb1-66" data-line-number="66"></a>
<a class="sourceLine" id="cb1-67" data-line-number="67"><span class="co">## Reference genome</span></a>
<a class="sourceLine" id="cb1-68" data-line-number="68">refPattern <-<span class="st"> "HuCoV2_WH01_2019"</span></a>
<a class="sourceLine" id="cb1-69" data-line-number="69"></a>
<a class="sourceLine" id="cb1-70" data-line-number="70"></a>
<a class="sourceLine" id="cb1-71" data-line-number="71"><span class="co">## Features : coordinates of features of interest in the reference genome</span></a>
<a class="sourceLine" id="cb1-72" data-line-number="72">features <-<span class="st"> </span><span class="kw">list</span>()</a>
<a class="sourceLine" id="cb1-73" data-line-number="73"><span class="co">## Spike gene (coding for the spike protein)</span></a>
<a class="sourceLine" id="cb1-74" data-line-number="74">features[[<span class="st">'CDS-ORF1ab'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">266</span>, <span class="dt">end =</span> <span class="dv">21555</span>)</a>
<a class="sourceLine" id="cb1-75" data-line-number="75">features[[<span class="st">'CDS-S'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">21563</span>, <span class="dt">end =</span> <span class="dv">25384</span>)</a>
<a class="sourceLine" id="cb1-76" data-line-number="76">features[[<span class="st">'CDS-ORF3a'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">25393</span>, <span class="dt">end =</span> <span class="dv">26220</span>)</a>
<a class="sourceLine" id="cb1-77" data-line-number="77">features[[<span class="st">'CDS-E'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">26245</span>, <span class="dt">end =</span> <span class="dv">26472</span>)</a>
<a class="sourceLine" id="cb1-78" data-line-number="78">features[[<span class="st">'CDS-M'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">26523</span>, <span class="dt">end =</span> <span class="dv">27191</span>)</a>
<a class="sourceLine" id="cb1-79" data-line-number="79">features[[<span class="st">'CDS-ORF6'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">27202</span>, <span class="dt">end =</span> <span class="dv">27387</span>)</a>
<a class="sourceLine" id="cb1-80" data-line-number="80">features[[<span class="st">'CDS-ORF7a'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">27394</span>, <span class="dt">end =</span> <span class="dv">27759</span>)</a>
<a class="sourceLine" id="cb1-81" data-line-number="81">features[[<span class="st">'CDS-ORF8'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">27894</span>, <span class="dt">end =</span> <span class="dv">28259</span>)</a>
<a class="sourceLine" id="cb1-82" data-line-number="82">features[[<span class="st">'CDS-N'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">28274</span>, <span class="dt">end =</span> <span class="dv">29533</span>)</a>
<a class="sourceLine" id="cb1-83" data-line-number="83">features[[<span class="st">'CDS-ORF10'</span>]] <-<span class="st"> </span><span class="kw">c</span>(<span class="dt">start =</span> <span class="dv">29558</span>, <span class="dt">end =</span> <span class="dv">29674</span>) </a>
<a class="sourceLine" id="cb1-84" data-line-number="84"></a>
<a class="sourceLine" id="cb1-85" data-line-number="85"><span class="co">## Query genomes</span></a>
<a class="sourceLine" id="cb1-86" data-line-number="86">queryPatterns <-<span class="st"> </span><span class="kw">c</span>(</a>
<a class="sourceLine" id="cb1-87" data-line-number="87"> <span class="st">"BtRaTG13_2013_Yunnan"</span>, </a>
<a class="sourceLine" id="cb1-88" data-line-number="88"> <span class="st">"BtZC45"</span>,</a>
<a class="sourceLine" id="cb1-89" data-line-number="89"> <span class="st">"BtZXC21"</span>,</a>
<a class="sourceLine" id="cb1-90" data-line-number="90"> <span class="st">"PnMP789"</span>,</a>
<a class="sourceLine" id="cb1-91" data-line-number="91"> <span class="st">"PnGX-P1E_2017"</span>, </a>
<a class="sourceLine" id="cb1-92" data-line-number="92"> <span class="st">"HuSARS-Frankfurt-1_2003"</span>,</a>
<a class="sourceLine" id="cb1-93" data-line-number="93"> <span class="st">"BtRc-o319 LC556375.1_ref_genome"</span>,</a>
<a class="sourceLine" id="cb1-94" data-line-number="94"> <span class="st">"BtRacCS203 MW251308_ref_genome"</span>,</a>
<a class="sourceLine" id="cb1-95" data-line-number="95"> <span class="st">"BtRacCS264 MW251311_ref_genome"</span>,</a>
<a class="sourceLine" id="cb1-96" data-line-number="96"> <span class="st">"BtRacCS253 MW251310.1_ref_genome"</span>,</a>
<a class="sourceLine" id="cb1-97" data-line-number="97"> <span class="st">"BtRacCS224 MW251309.1_ref_genome"</span>,</a>
<a class="sourceLine" id="cb1-98" data-line-number="98"> <span class="st">"BtRacCS271 MW251312_genome"</span></a>
<a class="sourceLine" id="cb1-99" data-line-number="99">)</a>
<a class="sourceLine" id="cb1-100" data-line-number="100"></a>
<a class="sourceLine" id="cb1-101" data-line-number="101"><span class="co">#### Add GISAID IDs to the query pattern ####</span></a>
<a class="sourceLine" id="cb1-102" data-line-number="102"><span class="co">## Note that GISAI genomes are be submitted to the github repo because they cannot be redistributed</span></a>
<a class="sourceLine" id="cb1-103" data-line-number="103"><span class="cf">if</span> (useGISAID) {</a>
<a class="sourceLine" id="cb1-104" data-line-number="104"> queryPatterns <-<span class="st"> </span><span class="kw">append</span>(queryPatterns, </a>
<a class="sourceLine" id="cb1-105" data-line-number="105"> <span class="kw">c</span>(<span class="st">"BtYu-RmYN02_2019"</span>,</a>
<a class="sourceLine" id="cb1-106" data-line-number="106"> <span class="st">"PnGu1_2019"</span>,</a>
<a class="sourceLine" id="cb1-107" data-line-number="107"> <span class="st">"BtCambodia/RShSTT200/2010"</span>,</a>
<a class="sourceLine" id="cb1-108" data-line-number="108"> <span class="st">"BtCambodia/RShSTT182/2010"</span></a>
<a class="sourceLine" id="cb1-109" data-line-number="109"> ))</a>
<a class="sourceLine" id="cb1-110" data-line-number="110">}</a>
<a class="sourceLine" id="cb1-111" data-line-number="111"></a>
<a class="sourceLine" id="cb1-112" data-line-number="112"><span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">Reference genomes: "</span>, refPattern)</a>
<a class="sourceLine" id="cb1-113" data-line-number="113"><span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">Number of query patterns: "</span>, <span class="kw">length</span>(queryPatterns))</a>
<a class="sourceLine" id="cb1-114" data-line-number="114"><span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">Query patterns: "</span>, <span class="kw">paste</span>(<span class="dt">collapse =</span> <span class="st">", "</span>, queryPatterns))</a></code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="co">#### Load genome sequences ####</span></a>
<a class="sourceLine" id="cb2-2" data-line-number="2">genomes <-<span class="st"> </span><span class="kw">readDNAStringSet</span>(<span class="dt">filepath =</span> infiles<span class="op">$</span>genome, <span class="dt">format =</span> <span class="st">"fasta"</span>)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"></a>
<a class="sourceLine" id="cb2-4" data-line-number="4"><span class="co">## Shorten sequence names by suppressing the fasta comment (after the space)</span></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="kw">names</span>(genomes) <-<span class="st"> </span><span class="kw">sub</span>(<span class="dt">pattern =</span> <span class="st">" .*"</span>, <span class="dt">replacement =</span> <span class="st">""</span>, <span class="dt">x =</span> <span class="kw">names</span>(genomes), <span class="dt">perl =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb2-6" data-line-number="6"></a>
<a class="sourceLine" id="cb2-7" data-line-number="7">genomeNames <-<span class="st"> </span><span class="kw">names</span>(genomes)</a>
<a class="sourceLine" id="cb2-8" data-line-number="8">nbGenomes <-<span class="st"> </span><span class="kw">length</span>(genomeNames)</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="kw">message</span>(<span class="st">"Loaded "</span>, nbGenomes, <span class="st">" genomes from file "</span>, infiles<span class="op">$</span>genomes)</a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># View(genomes)</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co">#### Define reference and query genomes ####</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13">refGenomeName <-<span class="st"> </span><span class="kw">grep</span>(<span class="dt">pattern =</span> refPattern, <span class="dt">x =</span> <span class="kw">names</span>(genomes), </a>
<a class="sourceLine" id="cb2-14" data-line-number="14"> <span class="dt">ignore.case =</span> <span class="ot">TRUE</span>, <span class="dt">value =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="cf">if</span> (<span class="kw">is.null</span>(refGenomeName)) {</a>
<a class="sourceLine" id="cb2-16" data-line-number="16"> <span class="kw">stop</span>(<span class="st">"Could not identify reference genome with pattern "</span>, refPattern)</a>
<a class="sourceLine" id="cb2-17" data-line-number="17">}</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="kw">message</span>(<span class="st">"Reference genome name: "</span>, refGenomeName)</a>
<a class="sourceLine" id="cb2-19" data-line-number="19"></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co">## Query genomes</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21">queryRegExp <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"("</span>, <span class="kw">paste</span>(<span class="dt">collapse =</span> <span class="st">")|("</span>, queryPatterns), <span class="st">")"</span>)</a>
<a class="sourceLine" id="cb2-22" data-line-number="22">queryGenomeNames <-<span class="st"> </span><span class="kw">grep</span>(<span class="dt">pattern =</span> queryRegExp, </a>
<a class="sourceLine" id="cb2-23" data-line-number="23"> <span class="dt">x =</span> genomeNames, </a>
<a class="sourceLine" id="cb2-24" data-line-number="24"> <span class="dt">ignore.case =</span> <span class="ot">TRUE</span>, <span class="dt">value =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb2-25" data-line-number="25">nbQueryGenomes <-<span class="st"> </span><span class="kw">length</span>(queryGenomeNames)</a>
<a class="sourceLine" id="cb2-26" data-line-number="26"></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="cf">if</span> (nbQueryGenomes <span class="op">==</span><span class="st"> </span><span class="dv">0</span>) {</a>
<a class="sourceLine" id="cb2-28" data-line-number="28"> <span class="kw">stop</span>(<span class="st">"Could not identify any query genome with query pattern</span><span class="ch">\n</span><span class="st">"</span>, queryRegExp)</a>
<a class="sourceLine" id="cb2-29" data-line-number="29">}</a>
<a class="sourceLine" id="cb2-30" data-line-number="30"></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="cf">if</span> (<span class="kw">length</span>(queryPatterns) <span class="op">!=</span><span class="st"> </span><span class="kw">length</span>(queryGenomeNames)) {</a>
<a class="sourceLine" id="cb2-32" data-line-number="32"> foundPatterns <-<span class="st"> </span><span class="kw">grep</span>(<span class="dt">pattern =</span> queryRegExp, <span class="dt">x =</span> queryGenomeNames, <span class="dt">value =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb2-33" data-line-number="33"> missingPatterns <-<span class="st"> </span><span class="kw">setdiff</span>(queryPatterns, queryGenomeNames)</a>
<a class="sourceLine" id="cb2-34" data-line-number="34"> <span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">"</span>, </a>
<a class="sourceLine" id="cb2-35" data-line-number="35"> <span class="kw">length</span>(missingPatterns), <span class="st">" Missing genomes: "</span>, </a>
<a class="sourceLine" id="cb2-36" data-line-number="36"> <span class="kw">paste</span>(<span class="dt">collapse =</span> <span class="st">", "</span>, missingPatterns))</a>
<a class="sourceLine" id="cb2-37" data-line-number="37">}</a>
<a class="sourceLine" id="cb2-38" data-line-number="38"></a>
<a class="sourceLine" id="cb2-39" data-line-number="39"></a>
<a class="sourceLine" id="cb2-40" data-line-number="40"><span class="co">## Compute some statistics about genome sizes</span></a>
<a class="sourceLine" id="cb2-41" data-line-number="41">genomeStat <-<span class="st"> </span><span class="kw">data.frame</span>(</a>
<a class="sourceLine" id="cb2-42" data-line-number="42"> <span class="dt">row.names =</span> <span class="kw">c</span>(refGenomeName, queryGenomeNames),</a>
<a class="sourceLine" id="cb2-43" data-line-number="43"> <span class="dt">status =</span> <span class="kw">c</span>(<span class="st">"Reference"</span>, <span class="kw">rep</span>(<span class="st">"Query"</span>, <span class="dt">length.out =</span> <span class="kw">length</span>(queryGenomeNames)))</a>
<a class="sourceLine" id="cb2-44" data-line-number="44">)</a>
<a class="sourceLine" id="cb2-45" data-line-number="45"></a>
<a class="sourceLine" id="cb2-46" data-line-number="46">g <-<span class="st"> </span><span class="dv">1</span></a>
<a class="sourceLine" id="cb2-47" data-line-number="47"><span class="cf">for</span> (g <span class="cf">in</span> <span class="kw">c</span>(refGenomeName, queryGenomeNames)) {</a>
<a class="sourceLine" id="cb2-48" data-line-number="48"> genomeStat[g, <span class="st">"length"</span>] <-<span class="st"> </span><span class="kw">length</span>(genomes[[g]])</a>
<a class="sourceLine" id="cb2-49" data-line-number="49">}</a>
<a class="sourceLine" id="cb2-50" data-line-number="50"></a>
<a class="sourceLine" id="cb2-51" data-line-number="51"><span class="kw">kable</span>(genomeStat, <span class="dt">caption =</span> <span class="st">"Reference and query genomes"</span>)</a></code></pre></div>
<table>
<caption>Reference and query genomes</caption>
<thead>
<tr class="header">
<th align="left"></th>
<th align="left">status</th>
<th align="right">length</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">HuCoV2_WH01_2019</td>
<td align="left">Reference</td>
<td align="right">29899</td>
</tr>
<tr class="even">
<td align="left">BtRaTG13_2013_Yunnan</td>
<td align="left">Query</td>
<td align="right">29855</td>
</tr>
<tr class="odd">
<td align="left">BtZC45</td>
<td align="left">Query</td>
<td align="right">29802</td>
</tr>
<tr class="even">
<td align="left">BtZXC21</td>
<td align="left">Query</td>
<td align="right">29732</td>
</tr>
<tr class="odd">
<td align="left">HuSARS-Frankfurt-1_2003</td>
<td align="left">Query</td>
<td align="right">29727</td>
</tr>
<tr class="even">
<td align="left">PnGX-P1E_2017</td>
<td align="left">Query</td>
<td align="right">29801</td>
</tr>
<tr class="odd">
<td align="left">PnMP789</td>
<td align="left">Query</td>
<td align="right">29521</td>
</tr>
<tr class="even">
<td align="left">BtYu-RmYN02_2019</td>
<td align="left">Query</td>
<td align="right">29671</td>
</tr>
<tr class="odd">
<td align="left">PnGu1_2019</td>
<td align="left">Query</td>
<td align="right">29825</td>
</tr>
<tr class="even">
<td align="left">BtCambodia/RShSTT200/2010</td>
<td align="left">Query</td>
<td align="right">29793</td>
</tr>
<tr class="odd">
<td align="left">BtCambodia/RShSTT182/2010</td>
<td align="left">Query</td>
<td align="right">29787</td>
</tr>
</tbody>
</table>
<p>The collection around-CoV-2 contains 26 virus genome sequences.</p>
<div id="strain-statistics" class="section level2">
<h2>Strain statistics</h2>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="co">## Report the number of genoomes</span></a>
<a class="sourceLine" id="cb3-2" data-line-number="2">strainNames <-<span class="st"> </span><span class="kw">names</span>(genomes)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3">nbStrains <-<span class="st"> </span><span class="kw">length</span>(strainNames)</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">Loaded "</span>, nbStrains, <span class="st">" genomes from file "</span>, infiles<span class="op">$</span>sequences)</a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># View(genomes)</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#### Define reference and query genomes ####</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9">refStrainName <-<span class="st"> </span><span class="kw">grep</span>(<span class="dt">pattern =</span> refPattern, <span class="dt">x =</span> <span class="kw">names</span>(genomes), </a>
<a class="sourceLine" id="cb3-10" data-line-number="10"> <span class="dt">ignore.case =</span> <span class="ot">TRUE</span>, <span class="dt">value =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="cf">if</span> (<span class="kw">is.null</span>(refStrainName)) {</a>
<a class="sourceLine" id="cb3-12" data-line-number="12"> <span class="kw">stop</span>(<span class="st">"Could not identify reference genome with pattern "</span>, refPattern)</a>
<a class="sourceLine" id="cb3-13" data-line-number="13">}</a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="kw">message</span>(<span class="st">"</span><span class="ch">\t</span><span class="st">Reference genome name: "</span>, refStrainName)</a>
<a class="sourceLine" id="cb3-15" data-line-number="15"></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co">#### Compute statistics about sequence sizes </span><span class="al">###</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17">strainStats <-<span class="st"> </span><span class="kw">data.frame</span>(</a>
<a class="sourceLine" id="cb3-18" data-line-number="18"> <span class="dt">n =</span> <span class="dv">1</span><span class="op">:</span><span class="kw">length</span>(genomes),</a>
<a class="sourceLine" id="cb3-19" data-line-number="19"> <span class="dt">row.names =</span> <span class="kw">names</span>(genomes),</a>
<a class="sourceLine" id="cb3-20" data-line-number="20"> <span class="dt">status =</span> <span class="kw">rep</span>(<span class="st">"Query"</span>, <span class="dt">length.out =</span> <span class="kw">length</span>(strainNames))</a>
<a class="sourceLine" id="cb3-21" data-line-number="21">)</a>
<a class="sourceLine" id="cb3-22" data-line-number="22">strainStats[,<span class="st">"status"</span>] <-<span class="st"> </span><span class="kw">as.vector</span>(strainStats[,<span class="st">"status"</span>])</a>
<a class="sourceLine" id="cb3-23" data-line-number="23">strainStats[refStrainName,<span class="st">"status"</span>] <-<span class="st"> "Reference"</span></a>
<a class="sourceLine" id="cb3-24" data-line-number="24">g <-<span class="st"> </span><span class="dv">1</span></a>
<a class="sourceLine" id="cb3-25" data-line-number="25"><span class="cf">for</span> (g <span class="cf">in</span> strainNames) {</a>
<a class="sourceLine" id="cb3-26" data-line-number="26"> strainStats[g, <span class="st">"length"</span>] <-<span class="st"> </span><span class="kw">length</span>(genomes[[g]])</a>
<a class="sourceLine" id="cb3-27" data-line-number="27">}</a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co">#### Define the color associated to each sequence ####</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"></a>
<a class="sourceLine" id="cb4-3" data-line-number="3"></a>
<a class="sourceLine" id="cb4-4" data-line-number="4"><span class="co">## Color palette per species</span></a>
<a class="sourceLine" id="cb4-5" data-line-number="5">speciesPalette <-<span class="st"> </span><span class="kw">list</span>(</a>
<a class="sourceLine" id="cb4-6" data-line-number="6"> <span class="dt">Human =</span> <span class="st">"#880000"</span>,</a>
<a class="sourceLine" id="cb4-7" data-line-number="7"> <span class="dt">Bat =</span> <span class="st">"#888888"</span>,</a>
<a class="sourceLine" id="cb4-8" data-line-number="8"> <span class="dt">Pangolin =</span> <span class="st">"#448800"</span>,</a>
<a class="sourceLine" id="cb4-9" data-line-number="9"> <span class="dt">Camel =</span> <span class="st">"#BB8800"</span>,</a>
<a class="sourceLine" id="cb4-10" data-line-number="10"> <span class="dt">Pig =</span> <span class="st">"#FFBBBB"</span>,</a>
<a class="sourceLine" id="cb4-11" data-line-number="11"> <span class="dt">Civet =</span> <span class="st">"#00BBFF"</span></a>
<a class="sourceLine" id="cb4-12" data-line-number="12">)</a>
<a class="sourceLine" id="cb4-13" data-line-number="13"></a>
<a class="sourceLine" id="cb4-14" data-line-number="14"><span class="co">## Species prefix in the tip labels</span></a>
<a class="sourceLine" id="cb4-15" data-line-number="15">speciesPrefix <-<span class="st"> </span><span class="kw">c</span>(<span class="st">"Hu"</span> =<span class="st"> "Human"</span>,</a>
<a class="sourceLine" id="cb4-16" data-line-number="16"> <span class="st">"Bt"</span> =<span class="st"> "Bat"</span>,</a>
<a class="sourceLine" id="cb4-17" data-line-number="17"> <span class="st">"Pn"</span> =<span class="st"> "Pangolin"</span>,</a>
<a class="sourceLine" id="cb4-18" data-line-number="18"> <span class="st">"Cm"</span> =<span class="st"> "Camel"</span>,</a>
<a class="sourceLine" id="cb4-19" data-line-number="19"> <span class="st">"Pi"</span> =<span class="st"> "Pig"</span>,</a>
<a class="sourceLine" id="cb4-20" data-line-number="20"> <span class="st">"Cv"</span> =<span class="st"> "Civet"</span>)</a>
<a class="sourceLine" id="cb4-21" data-line-number="21"></a>
<a class="sourceLine" id="cb4-22" data-line-number="22"><span class="co">## Strain-specific colors</span></a>
<a class="sourceLine" id="cb4-23" data-line-number="23">strainColor <-<span class="st"> </span><span class="kw">c</span>(</a>
<a class="sourceLine" id="cb4-24" data-line-number="24"> <span class="st">"HuCoV2_WH01_2019"</span> =<span class="st"> "red"</span>,</a>
<a class="sourceLine" id="cb4-25" data-line-number="25"> <span class="st">"HuSARS-Frankfurt-1_2003"</span> =<span class="st"> "#0044BB"</span>,</a>
<a class="sourceLine" id="cb4-26" data-line-number="26"> <span class="st">"PnGu1_2019"</span> =<span class="st"> "#00BB00"</span>,</a>
<a class="sourceLine" id="cb4-27" data-line-number="27"> <span class="st">"PnMP789"</span> =<span class="st"> "#00FF88"</span>,</a>
<a class="sourceLine" id="cb4-28" data-line-number="28"> <span class="st">"BtRaTG13_"</span> =<span class="st"> "#FF6600"</span>,</a>
<a class="sourceLine" id="cb4-29" data-line-number="29"> <span class="st">"BtYu-RmYN"</span> =<span class="st"> "#FFBB22"</span>,</a>
<a class="sourceLine" id="cb4-30" data-line-number="30"> <span class="st">"BtZXC21"</span> =<span class="st"> "black"</span>, </a>
<a class="sourceLine" id="cb4-31" data-line-number="31"> <span class="st">"BtZC45"</span> =<span class="st"> "black"</span>)</a>
<a class="sourceLine" id="cb4-32" data-line-number="32"></a>
<a class="sourceLine" id="cb4-33" data-line-number="33"><span class="co">## Identify species per tip</span></a>
<a class="sourceLine" id="cb4-34" data-line-number="34"><span class="cf">for</span> (prefix <span class="cf">in</span> <span class="kw">names</span>(speciesPrefix)) {</a>
<a class="sourceLine" id="cb4-35" data-line-number="35"> strainStats[<span class="kw">grep</span>(<span class="dt">pattern =</span> <span class="kw">paste0</span>(<span class="st">"^"</span>, prefix), <span class="dt">x =</span> <span class="kw">row.names</span>(strainStats), <span class="dt">perl =</span> <span class="ot">TRUE</span>), <span class="st">"species"</span>] <-<span class="st"> </span>speciesPrefix[prefix]</a>
<a class="sourceLine" id="cb4-36" data-line-number="36"> </a>
<a class="sourceLine" id="cb4-37" data-line-number="37">}</a>
<a class="sourceLine" id="cb4-38" data-line-number="38"></a>
<a class="sourceLine" id="cb4-39" data-line-number="39"><span class="co">## Assign acolor to each species</span></a>
<a class="sourceLine" id="cb4-40" data-line-number="40">strainStats<span class="op">$</span>color <-<span class="st"> "grey"</span> <span class="co"># default</span></a>
<a class="sourceLine" id="cb4-41" data-line-number="41">strainStats<span class="op">$</span>color <-<span class="st"> </span>speciesPalette[<span class="kw">as.vector</span>(strainStats<span class="op">$</span>species)]</a>
<a class="sourceLine" id="cb4-42" data-line-number="42"></a>
<a class="sourceLine" id="cb4-43" data-line-number="43"><span class="cf">for</span> (strain <span class="cf">in</span> <span class="kw">names</span>(strainColor)) {</a>
<a class="sourceLine" id="cb4-44" data-line-number="44"> strainStats[<span class="kw">grep</span>(<span class="dt">pattern =</span> <span class="kw">paste0</span>(<span class="st">"^"</span>, strain), </a>
<a class="sourceLine" id="cb4-45" data-line-number="45"> <span class="dt">x =</span> <span class="kw">row.names</span>(strainStats), <span class="dt">perl =</span> <span class="ot">TRUE</span>), <span class="st">"color"</span>] <-<span class="st"> </span>strainColor[strain]</a>
<a class="sourceLine" id="cb4-46" data-line-number="46"> </a>
<a class="sourceLine" id="cb4-47" data-line-number="47">}</a>
<a class="sourceLine" id="cb4-48" data-line-number="48"></a>
<a class="sourceLine" id="cb4-49" data-line-number="49"></a>
<a class="sourceLine" id="cb4-50" data-line-number="50"><span class="co">## Assign specific color to some nodes</span></a>
<a class="sourceLine" id="cb4-51" data-line-number="51"></a>
<a class="sourceLine" id="cb4-52" data-line-number="52"><span class="co">## Define a color for each strain</span></a>
<a class="sourceLine" id="cb4-53" data-line-number="53">strainColors <-<span class="st"> </span>(<span class="kw">unlist</span>(strainStats<span class="op">$</span>color))</a>
<a class="sourceLine" id="cb4-54" data-line-number="54"><span class="kw">names</span>(strainColors) <-<span class="st"> </span><span class="kw">row.names</span>(strainStats)</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">kable</span>(strainStats, <span class="dt">caption =</span> <span class="st">"Reference and query genomes"</span>)</a></code></pre></div>
<table>
<caption>Reference and query genomes</caption>
<thead>
<tr class="header">
<th align="left"></th>
<th align="right">n</th>
<th align="left">status</th>
<th align="right">length</th>
<th align="left">species</th>
<th align="left">color</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">BtBM48-31</td>
<td align="right">1</td>
<td align="left">Query</td>
<td align="right">29276</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtGX2013</td>
<td align="right">2</td>
<td align="left">Query</td>
<td align="right">29161</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="odd">
<td align="left">BtHKU3-12</td>
<td align="right">3</td>
<td align="left">Query</td>
<td align="right">29704</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtRaTG13_2013_Yunnan</td>
<td align="right">4</td>
<td align="left">Query</td>
<td align="right">29855</td>
<td align="left">Bat</td>
<td align="left">#FF6600</td>
</tr>
<tr class="odd">
<td align="left">BtRs4874</td>
<td align="right">5</td>
<td align="left">Query</td>
<td align="right">30311</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtYN2013</td>
<td align="right">6</td>
<td align="left">Query</td>
<td align="right">29142</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="odd">
<td align="left">BtYN2018B</td>
<td align="right">7</td>
<td align="left">Query</td>
<td align="right">30256</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtZC45</td>
<td align="right">8</td>
<td align="left">Query</td>
<td align="right">29802</td>
<td align="left">Bat</td>
<td align="left">black</td>
</tr>
<tr class="odd">
<td align="left">BtZXC21</td>
<td align="right">9</td>
<td align="left">Query</td>
<td align="right">29732</td>
<td align="left">Bat</td>
<td align="left">black</td>
</tr>
<tr class="even">
<td align="left">Cv007-2004</td>
<td align="right">10</td>
<td align="left">Query</td>
<td align="right">29540</td>
<td align="left">Civet</td>
<td align="left">#00BBFF</td>
</tr>
<tr class="odd">
<td align="left">HuCoV2_WH01_2019</td>
<td align="right">11</td>
<td align="left">Reference</td>
<td align="right">29899</td>
<td align="left">Human</td>
<td align="left">red</td>
</tr>
<tr class="even">
<td align="left">HuSARS-Frankfurt-1_2003</td>
<td align="right">12</td>
<td align="left">Query</td>
<td align="right">29727</td>
<td align="left">Human</td>
<td align="left">#0044BB</td>
</tr>
<tr class="odd">
<td align="left">PnGX-P1E_2017</td>
<td align="right">13</td>
<td align="left">Query</td>
<td align="right">29801</td>
<td align="left">Pangolin</td>
<td align="left">#448800</td>
</tr>
<tr class="even">
<td align="left">PnGX-P2V_2018</td>
<td align="right">14</td>
<td align="left">Query</td>
<td align="right">29795</td>
<td align="left">Pangolin</td>
<td align="left">#448800</td>
</tr>
<tr class="odd">
<td align="left">PnMP789</td>
<td align="right">15</td>
<td align="left">Query</td>
<td align="right">29521</td>
<td align="left">Pangolin</td>
<td align="left">#00FF88</td>
</tr>
<tr class="even">
<td align="left">BtRc-o319</td>
<td align="right">16</td>
<td align="left">Query</td>
<td align="right">29718</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="odd">
<td align="left">BtRacCS203</td>
<td align="right">17</td>
<td align="left">Query</td>
<td align="right">29832</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtRacCS264</td>
<td align="right">18</td>
<td align="left">Query</td>
<td align="right">29820</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="odd">
<td align="left">BtRacCS253</td>
<td align="right">19</td>
<td align="left">Query</td>
<td align="right">29820</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtRacCS224</td>
<td align="right">20</td>
<td align="left">Query</td>
<td align="right">29820</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="odd">
<td align="left">BtRacCS271</td>
<td align="right">21</td>
<td align="left">Query</td>
<td align="right">29820</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtYu-RmYN02_2019</td>
<td align="right">22</td>
<td align="left">Query</td>
<td align="right">29671</td>
<td align="left">Bat</td>
<td align="left">#FFBB22</td>
</tr>
<tr class="odd">
<td align="left">PnGu1_2019</td>
<td align="right">23</td>
<td align="left">Query</td>
<td align="right">29825</td>
<td align="left">Pangolin</td>
<td align="left">#00BB00</td>
</tr>
<tr class="even">
<td align="left">PnGu-P2S_2019</td>
<td align="right">24</td>
<td align="left">Query</td>
<td align="right">29769</td>
<td align="left">Pangolin</td>
<td align="left">#448800</td>
</tr>
<tr class="odd">
<td align="left">BtCambodia/RShSTT200/2010</td>
<td align="right">25</td>
<td align="left">Query</td>
<td align="right">29793</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
<tr class="even">
<td align="left">BtCambodia/RShSTT182/2010</td>
<td align="right">26</td>
<td align="left">Query</td>
<td align="right">29787</td>
<td align="left">Bat</td>
<td align="left">#888888</td>
</tr>
</tbody>
</table>
</div>
<div id="n-to-1-full-genome-alignments" class="section level2">
<h2>N-to-1 full genome alignments</h2>
<p>We perform a pairwise lignment between each genome query and the reference genome (HuCoV2_WH01_2019).</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="co">#### N-to-1 genome alignments ####</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="co">## Define output file for genome alignments</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4">outfiles[<span class="st">"Genome alignments"</span>] <-<span class="st"> </span><span class="kw">file.path</span>(</a>
<a class="sourceLine" id="cb6-5" data-line-number="5"> dir<span class="op">$</span>outseq, <span class="kw">paste0</span>(<span class="st">"genome_alignments_ref_"</span>, refGenomeName))</a>
<a class="sourceLine" id="cb6-6" data-line-number="6"></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co">## Get sequences for reference and query genomes</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8">refGenome <-<span class="st"> </span>genomes[refGenomeName]</a>
<a class="sourceLine" id="cb6-9" data-line-number="9">queryGenomes <-<span class="st"> </span>genomes[queryGenomeNames]</a>
<a class="sourceLine" id="cb6-10" data-line-number="10">genomesNto1 <-<span class="st"> </span><span class="kw">alignNtoOne</span>(</a>
<a class="sourceLine" id="cb6-11" data-line-number="11"> <span class="dt">refSequence =</span> refGenome, </a>
<a class="sourceLine" id="cb6-12" data-line-number="12"> <span class="dt">querySequences =</span> queryGenomes,</a>
<a class="sourceLine" id="cb6-13" data-line-number="13"> <span class="dt">outfile =</span> outfiles[[<span class="st">"Genome alignments"</span>]] )</a>
<a class="sourceLine" id="cb6-14" data-line-number="14"></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="kw">kable</span>(genomesNto1<span class="op">$</span>stats[<span class="kw">order</span>(genomesNto1<span class="op">$</span>stats<span class="op">$</span>score, <span class="dt">decreasing =</span> <span class="ot">TRUE</span>), ], </a>
<a class="sourceLine" id="cb6-16" data-line-number="16"> <span class="dt">caption =</span> <span class="st">"N-to-one alignment of full genomes"</span>)</a></code></pre></div>
<table>
<caption>N-to-one alignment of full genomes</caption>
<thead>
<tr class="header">
<th align="left"></th>
<th align="right">pid</th>
<th align="right">nchar</th>
<th align="right">insertNb</th>
<th align="right">insertLen</th>
<th align="right">delNb</th>
<th align="right">delLen</th>
<th align="right">score</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">BtRaTG13_2013_Yunnan</td>
<td align="right">96.07482</td>
<td align="right">29884</td>
<td align="right">6</td>
<td align="right">29</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">49895.67</td>
</tr>
<tr class="even">
<td align="left">BtYu-RmYN02_2019</td>
<td align="right">93.70042</td>
<td align="right">29875</td>
<td align="right">59</td>
<td align="right">204</td>
<td align="right">22</td>
<td align="right">46</td>
<td align="right">43735.11</td>
</tr>
<tr class="odd">
<td align="left">BtCambodia/RShSTT200/2010</td>
<td align="right">92.86120</td>
<td align="right">29921</td>
<td align="right">19</td>
<td align="right">128</td>
<td align="right">12</td>
<td align="right">22</td>
<td align="right">42433.08</td>
</tr>
<tr class="even">
<td align="left">BtCambodia/RShSTT182/2010</td>
<td align="right">92.86311</td>
<td align="right">29915</td>
<td align="right">19</td>
<td align="right">128</td>
<td align="right">12</td>
<td align="right">22</td>
<td align="right">42395.07</td>
</tr>
<tr class="odd">
<td align="left">PnGu1_2019</td>
<td align="right">90.25891</td>
<td align="right">29894</td>
<td align="right">16</td>
<td align="right">69</td>
<td align="right">9</td>
<td align="right">23</td>
<td align="right">36100.06</td>
</tr>
<tr class="even">
<td align="left">PnMP789</td>
<td align="right">90.00945</td>
<td align="right">29638</td>
<td align="right">17</td>