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	<title><![CDATA[BOL: Understanding BLASTn output format 6 !]]></title>
	<link>https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6?</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</guid>
	<pubDate>Wed, 27 Jun 2018 18:38:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</link>
	<title><![CDATA[Understanding BLASTn output format 6 !]]></title>
	<description><![CDATA[<h3 id="sites-page-title-header" style="text-align: left;"><span>BLASTn output format 6</span></h3><div id="sites-canvas-main"><div id="sites-canvas-main-content"><div dir="ltr"><div><div><em>BLASTn</em> maps DNA against DNA, for example gene sequences against a reference genome<br /><br /><code><strong>blastn</strong>  -query <span>genes.ffn</span>  -subject <span>genome.fna</span>  -outfmt <strong>6</strong></code></div><h2>BLASTn tabular output format 6</h2>
<p><strong>Column headers:</strong><br /><code>qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore</code><br /></p>
<table border="1" cellspacing="0">
<tbody>
<tr>
<td> 1.</td>
<td> qseqid</td>
<td> query (e.g., gene) sequence id</td>
</tr>
<tr>
<td> 2.</td>
<td> sseqid</td>
<td> subject (e.g., reference genome) sequence id</td>
</tr>
<tr>
<td> 3.</td>
<td> pident</td>
<td> percentage of identical matches</td>
</tr>
<tr>
<td> 4.</td>
<td> length</td>
<td> alignment length</td>
</tr>
<tr>
<td> 5.</td>
<td> mismatch</td>
<td> number of mismatches</td>
</tr>
<tr>
<td> 6.</td>
<td> gapopen</td>
<td> number of gap openings</td>
</tr>
<tr>
<td> 7.</td>
<td> qstart</td>
<td> start of alignment in query</td>
</tr>
<tr>
<td> 8.</td>
<td> qend</td>
<td> end of alignment in query</td>
</tr>
<tr>
<td> 9.</td>
<td> sstart</td>
<td> start of alignment in subject</td>
</tr>
<tr>
<td> 10.</td>
<td> send</td>
<td> end of alignment in subject</td>
</tr>
<tr>
<td> 11.</td>
<td> evalue</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue">expect value</a></td>
</tr>
<tr>
<td> 12.</td>
<td> bitscore</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue"><strong>bit score</strong></a></td>
</tr>
</tbody>
</table>
<p><strong><br /></strong></p>
</div><h2><a name="TOC-Define-your-own-output-format" id="TOC-Define-your-own-output-format"></a>Define your own output format</h2><div><em>by adding the option -outfmt, as for example: </em><strong><br /></strong></div>
<p><code><strong>-outfmt</strong> <strong>"6</strong> <span>qseqid sseqid pident qlen length mismatch gapope evalue bitscore</span><strong>"</strong></code><br /><br /><em><strong>supported format specifiers are:</strong></em><br /><code>qseqid    </code>Query Seq-id<br /><code>qgi       </code>Query GI<br /><code>qacc      </code>Query accesion<br /><code>qaccver   </code>Query accesion.version<br /><code>qlen      </code>Query sequence length<br /><code>sseqid    </code>Subject Seq-id<br /><code>sallseqid </code>All subject Seq-id(s), separated by a ';'<br /><code>sgi       </code>Subject GI<br /><code>sallgi    </code>All subject GIs<br /><code>sacc      </code>Subject accession<br /><code>saccver   </code>Subject accession.version<br /><code>sallacc   </code>All subject accessions<br /><code>slen      </code>Subject sequence length<br /><code>qstart    </code>Start of alignment in query<br /><code>qend      </code>End of alignment in query<br /><code>sstart    </code>Start of alignment in subject<br /><code>send      </code>End of alignment in subject<br /><code>qseq      </code>Aligned part of query sequence<br /><code>sseq      </code>Aligned part of subject sequence<br /><code>evalue    </code>Expect value<br /><code>bitscore  </code>Bit score<br /><code>score     </code>Raw score<br /><code>length    </code>Alignment length<br /><code>pident    </code>Percentage of identical matches<br /><code>nident    </code>Number of identical matches<br /><code>mismatch  </code>Number of mismatches<br /><code>positive  </code>Number of positive-scoring matches<br /><code>gapopen   </code>Number of gap openings<br /><code>gaps      </code>Total number of gaps<br /><code>ppos      </code>Percentage of positive-scoring matches<br /><code>frames    </code>Query and subject frames separated by a '/'<br /><code>qframe    </code>Query frame<br /><code>sframe    </code>Subject frame<br /><code>btop      </code>Blast traceback operations (BTOP)<br /><code>staxids   </code>Subject Taxonomy ID(s), separated by a ';'<br /><code>sscinames </code>Subject Scientific Name(s), separated by a ';'<br /><code>scomnames </code>Subject Common Name(s), separated by a ';'<br /><code>sblastnames </code>Subject Blast Name(s), separated by a ';'   (in alphabetical order)<br /><code>sskingdoms  </code>Subject Super Kingdom(s), separated by a ';'     (in alphabetical order) <br /><code>stitle      </code>Subject Title<br /><code>salltitles  </code>All Subject Title(s), separated by a '&lt;&gt;'<br /><code>sstrand   </code>Subject Strand<br /><code>qcovs     </code>Query Coverage Per Subject<br /><code>qcovhsp   </code>Query Coverage Per HSP<br /><strong><br /><em>default values are:</em></strong><br /><code><code>-outfmt "</code>6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"</code></p>
</div></div></div>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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