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planemo upload for repository https://github.com/scottx611x/qualimap2 commit 070be0ead8afa05bfbb3075f075a97e7c32d619e-dirty
author scottx611x
date Thu, 26 Jul 2018 11:23:26 -0400
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4:10a0b8ee05fc 5:5cdadbdf021f
1 <!DOCTYPE HTML>
2 <html>
3 <head>
4 <link rel="stylesheet" href="css/agogo.css" type="text/css" />
5 <link rel="stylesheet" href="css/report.css" type="text/css" />
6 <title>Qualimap report: BAM QC</title>
7
8 </head>
9 <body>
10 <div class="header-wrapper">
11 <div class="header">
12 <p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
13 <img class="logo" src="css/qualimap_logo_small.png" alt="Logo"/>
14 </a></p>
15 <div class="headertitle"><a href="">Qualimap Report: BAM QC</a></div>
16 </div>
17 </div>
18
19 <div class="content-wrapper">
20 <div class="content">
21 <div class="document">
22 <div class="documentwrapper">
23 <div class="bodywrapper">
24 <div class="body">
25 <div class=section>
26 <h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline">&nbsp;</a></h2>
27 <div class=summary>
28
29
30 <div class=table-summary>
31 <h3>QualiMap command line</h3>
32 <table class="summary hovertable">
33 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
34 <td class=column1>qualimap bamqc -bam /mnt/galaxy/files/001/dataset_1209.dat -nw 400 -hm 3</td>
35 </tr>
36 </table>
37 </div>
38
39
40 <div class=table-summary>
41 <h3>Alignment</h3>
42 <table class="summary hovertable">
43 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
44 <td class=column1>Command line: </td>
45 <td class=column2>bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta</td>
46 </tr>
47 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
48 <td class=column1>Draw chromosome limits: </td>
49 <td class=column2>no
50 </td>
51 </tr>
52 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
53 <td class=column1>Analyze overlapping paired-end reads:</td>
54 <td class=column2>no
55 </td>
56 </tr>
57 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
58 <td class=column1>Program: </td>
59 <td class=column2>bwamem (0.7.15-r1140)</td>
60 </tr>
61 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
62 <td class=column1>Analysis date: </td>
63 <td class=column2>Thu Jul 26 13:34:52 UTC 2018</td>
64 </tr>
65 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
66 <td class=column1>Size of a homopolymer: </td>
67 <td class=column2>3</td>
68 </tr>
69 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
70 <td class=column1>Skip duplicate alignments: </td>
71 <td class=column2>no
72 </td>
73 </tr>
74 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
75 <td class=column1>Number of windows: </td>
76 <td class=column2>400</td>
77 </tr>
78 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
79 <td class=column1>BAM file: </td>
80 <td class=column2>/mnt/galaxy/files/001/dataset_1209.dat</td>
81 </tr>
82 </table>
83 </div>
84
85 </div>
86 </div> <!-- summary section -->
87
88 <div class=section>
89 <h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline">&nbsp;</a></h2>
90 <div class=summary>
91
92
93 <div class=table-summary>
94 <h3>Globals</h3>
95 <table class="summary hovertable">
96 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
97 <td class=column1>Reference size</td>
98 <td class=column2>3,101,976,562</td>
99 </tr>
100 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
101 <td class=column1>Number of reads</td>
102 <td class=column2>61,169</td>
103 </tr>
104 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
105 <td class=column1>Mapped reads</td>
106 <td class=column2>60,246 / 98.49%</td>
107 </tr>
108 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
109 <td class=column1>Unmapped reads</td>
110 <td class=column2>923 / 1.51%</td>
111 </tr>
112 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
113 <td class=column1>Mapped paired reads</td>
114 <td class=column2>60,246 / 98.49%</td>
115 </tr>
116 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
117 <td class=column1>Mapped reads, first in pair</td>
118 <td class=column2>30,268 / 49.48%</td>
119 </tr>
120 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
121 <td class=column1>Mapped reads, second in pair</td>
122 <td class=column2>29,978 / 49.01%</td>
123 </tr>
124 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
125 <td class=column1>Mapped reads, both in pair</td>
126 <td class=column2>59,810 / 97.78%</td>
127 </tr>
128 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
129 <td class=column1>Mapped reads, singletons</td>
130 <td class=column2>436 / 0.71%</td>
131 </tr>
132 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
133 <td class=column1>Read min/max/mean length</td>
134 <td class=column2>250 / 250 / 250</td>
135 </tr>
136 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
137 <td class=column1>Duplicated reads (flagged)</td>
138 <td class=column2>48 / 0.08%</td>
139 </tr>
140 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
141 <td class=column1>Clipped reads</td>
142 <td class=column2>33,606 / 54.94%</td>
143 </tr>
144 </table>
145 </div>
146
147
148 <div class=table-summary>
149 <h3>ACGT Content</h3>
150 <table class="summary hovertable">
151 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
152 <td class=column1>Number/percentage of A's</td>
153 <td class=column2>3,912,917 / 29.53%</td>
154 </tr>
155 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
156 <td class=column1>Number/percentage of C's</td>
157 <td class=column2>2,699,395 / 20.37%</td>
158 </tr>
159 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
160 <td class=column1>Number/percentage of T's</td>
161 <td class=column2>3,942,019 / 29.75%</td>
162 </tr>
163 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
164 <td class=column1>Number/percentage of G's</td>
165 <td class=column2>2,694,640 / 20.34%</td>
166 </tr>
167 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
168 <td class=column1>Number/percentage of N's</td>
169 <td class=column2>0 / 0%</td>
170 </tr>
171 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
172 <td class=column1>GC Percentage</td>
173 <td class=column2>40.71%</td>
174 </tr>
175 </table>
176 </div>
177
178
179 <div class=table-summary>
180 <h3>Coverage</h3>
181 <table class="summary hovertable">
182 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
183 <td class=column1>Mean</td>
184 <td class=column2>0.0043</td>
185 </tr>
186 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
187 <td class=column1>Standard Deviation</td>
188 <td class=column2>0.0869</td>
189 </tr>
190 </table>
191 </div>
192
193
194 <div class=table-summary>
195 <h3>Mapping Quality</h3>
196 <table class="summary hovertable">
197 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
198 <td class=column1>Mean Mapping Quality</td>
199 <td class=column2>49.97</td>
200 </tr>
201 </table>
202 </div>
203
204
205 <div class=table-summary>
206 <h3>Insert size</h3>
207 <table class="summary hovertable">
208 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
209 <td class=column1>Mean</td>
210 <td class=column2>75,226.79</td>
211 </tr>
212 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
213 <td class=column1>Standard Deviation</td>
214 <td class=column2>2,849,315.96</td>
215 </tr>
216 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
217 <td class=column1>P25/Median/P75</td>
218 <td class=column2>339 / 427 / 535</td>
219 </tr>
220 </table>
221 </div>
222
223
224 <div class=table-summary>
225 <h3>Mismatches and indels</h3>
226 <table class="summary hovertable">
227 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
228 <td class=column1>General error rate</td>
229 <td class=column2>1.49%</td>
230 </tr>
231 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
232 <td class=column1>Mismatches</td>
233 <td class=column2>190,508</td>
234 </tr>
235 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
236 <td class=column1>Insertions</td>
237 <td class=column2>2,279</td>
238 </tr>
239 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
240 <td class=column1>Mapped reads with at least one insertion</td>
241 <td class=column2>3.3%</td>
242 </tr>
243 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
244 <td class=column1>Deletions</td>
245 <td class=column2>2,316</td>
246 </tr>
247 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
248 <td class=column1>Mapped reads with at least one deletion</td>
249 <td class=column2>3.41%</td>
250 </tr>
251 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
252 <td class=column1>Homopolymer indels</td>
253 <td class=column2>50.79%</td>
254 </tr>
255 </table>
256 </div>
257
258
259 <div class=table-summary>
260 <h3>Chromosome stats</h3>
261 <table class="summary hovertable">
262 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
263 <td><b>Name</b></td>
264 <td><b>Length</b></td>
265 <td><b>Mapped bases</b></td>
266 <td><b>Mean coverage</b></td>
267 <td><b>Standard deviation</b></td>
268 </tr>
269 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
270 <td>1</td>
271 <td>249250621</td>
272 <td>1063202</td>
273 <td>0.0043</td>
274 <td>0.1147</td>
275 </tr>
276 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
277 <td>2</td>
278 <td>243199373</td>
279 <td>1091086</td>
280 <td>0.0045</td>
281 <td>0.082</td>
282 </tr>
283 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
284 <td>3</td>
285 <td>198022430</td>
286 <td>906302</td>
287 <td>0.0046</td>
288 <td>0.0765</td>
289 </tr>
290 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
291 <td>4</td>
292 <td>191154276</td>
293 <td>899976</td>
294 <td>0.0047</td>
295 <td>0.088</td>
296 </tr>
297 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
298 <td>5</td>
299 <td>180915260</td>
300 <td>759318</td>
301 <td>0.0042</td>
302 <td>0.0739</td>
303 </tr>
304 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
305 <td>6</td>
306 <td>171115067</td>
307 <td>734471</td>
308 <td>0.0043</td>
309 <td>0.0752</td>
310 </tr>
311 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
312 <td>7</td>
313 <td>159138663</td>
314 <td>654165</td>
315 <td>0.0041</td>
316 <td>0.0773</td>
317 </tr>
318 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
319 <td>8</td>
320 <td>146364022</td>
321 <td>676934</td>
322 <td>0.0046</td>
323 <td>0.1184</td>
324 </tr>
325 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
326 <td>9</td>
327 <td>141213431</td>
328 <td>525097</td>
329 <td>0.0037</td>
330 <td>0.0766</td>
331 </tr>
332 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
333 <td>10</td>
334 <td>135534747</td>
335 <td>724777</td>
336 <td>0.0053</td>
337 <td>0.1311</td>
338 </tr>
339 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
340 <td>11</td>
341 <td>135006516</td>
342 <td>589118</td>
343 <td>0.0044</td>
344 <td>0.082</td>
345 </tr>
346 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
347 <td>12</td>
348 <td>133851895</td>
349 <td>581268</td>
350 <td>0.0043</td>
351 <td>0.0745</td>
352 </tr>
353 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
354 <td>13</td>
355 <td>115169878</td>
356 <td>424915</td>
357 <td>0.0037</td>
358 <td>0.0689</td>
359 </tr>
360 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
361 <td>14</td>
362 <td>107349540</td>
363 <td>385363</td>
364 <td>0.0036</td>
365 <td>0.068</td>
366 </tr>
367 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
368 <td>15</td>
369 <td>102531392</td>
370 <td>361006</td>
371 <td>0.0035</td>
372 <td>0.0671</td>
373 </tr>
374 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
375 <td>16</td>
376 <td>90354753</td>
377 <td>405846</td>
378 <td>0.0045</td>
379 <td>0.0833</td>
380 </tr>
381 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
382 <td>17</td>
383 <td>81195210</td>
384 <td>351366</td>
385 <td>0.0043</td>
386 <td>0.0765</td>
387 </tr>
388 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
389 <td>18</td>
390 <td>78077248</td>
391 <td>355035</td>
392 <td>0.0045</td>
393 <td>0.0817</td>
394 </tr>
395 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
396 <td>19</td>
397 <td>59128983</td>
398 <td>263166</td>
399 <td>0.0045</td>
400 <td>0.0888</td>
401 </tr>
402 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
403 <td>20</td>
404 <td>63025520</td>
405 <td>262814</td>
406 <td>0.0042</td>
407 <td>0.0805</td>
408 </tr>
409 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
410 <td>21</td>
411 <td>48129895</td>
412 <td>179259</td>
413 <td>0.0037</td>
414 <td>0.0748</td>
415 </tr>
416 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
417 <td>22</td>
418 <td>51304566</td>
419 <td>150578</td>
420 <td>0.0029</td>
421 <td>0.0612</td>
422 </tr>
423 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
424 <td>X</td>
425 <td>155270560</td>
426 <td>669025</td>
427 <td>0.0043</td>
428 <td>0.0753</td>
429 </tr>
430 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
431 <td>Y</td>
432 <td>59373566</td>
433 <td>28998</td>
434 <td>0.0005</td>
435 <td>0.049</td>
436 </tr>
437 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
438 <td>MT</td>
439 <td>16569</td>
440 <td>56251</td>
441 <td>3.395</td>
442 <td>2.0903</td>
443 </tr>
444 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
445 <td>GL000207.1</td>
446 <td>4262</td>
447 <td>0</td>
448 <td>0</td>
449 <td>0</td>
450 </tr>
451 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
452 <td>GL000226.1</td>
453 <td>15008</td>
454 <td>21953</td>
455 <td>1.4628</td>
456 <td>1.7817</td>
457 </tr>
458 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
459 <td>GL000229.1</td>
460 <td>19913</td>
461 <td>0</td>
462 <td>0</td>
463 <td>0</td>
464 </tr>
465 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
466 <td>GL000231.1</td>
467 <td>27386</td>
468 <td>1169</td>
469 <td>0.0427</td>
470 <td>0.2278</td>
471 </tr>
472 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
473 <td>GL000210.1</td>
474 <td>27682</td>
475 <td>0</td>
476 <td>0</td>
477 <td>0</td>
478 </tr>
479 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
480 <td>GL000239.1</td>
481 <td>33824</td>
482 <td>0</td>
483 <td>0</td>
484 <td>0</td>
485 </tr>
486 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
487 <td>GL000235.1</td>
488 <td>34474</td>
489 <td>0</td>
490 <td>0</td>
491 <td>0</td>
492 </tr>
493 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
494 <td>GL000201.1</td>
495 <td>36148</td>
496 <td>0</td>
497 <td>0</td>
498 <td>0</td>
499 </tr>
500 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
501 <td>GL000247.1</td>
502 <td>36422</td>
503 <td>0</td>
504 <td>0</td>
505 <td>0</td>
506 </tr>
507 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
508 <td>GL000245.1</td>
509 <td>36651</td>
510 <td>481</td>
511 <td>0.0131</td>
512 <td>0.1138</td>
513 </tr>
514 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
515 <td>GL000197.1</td>
516 <td>37175</td>
517 <td>0</td>
518 <td>0</td>
519 <td>0</td>
520 </tr>
521 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
522 <td>GL000203.1</td>
523 <td>37498</td>
524 <td>459</td>
525 <td>0.0122</td>
526 <td>0.1178</td>
527 </tr>
528 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
529 <td>GL000246.1</td>
530 <td>38154</td>
531 <td>0</td>
532 <td>0</td>
533 <td>0</td>
534 </tr>
535 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
536 <td>GL000249.1</td>
537 <td>38502</td>
538 <td>483</td>
539 <td>0.0125</td>
540 <td>0.1113</td>
541 </tr>
542 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
543 <td>GL000196.1</td>
544 <td>38914</td>
545 <td>0</td>
546 <td>0</td>
547 <td>0</td>
548 </tr>
549 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
550 <td>GL000248.1</td>
551 <td>39786</td>
552 <td>456</td>
553 <td>0.0115</td>
554 <td>0.1064</td>
555 </tr>
556 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
557 <td>GL000244.1</td>
558 <td>39929</td>
559 <td>0</td>
560 <td>0</td>
561 <td>0</td>
562 </tr>
563 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
564 <td>GL000238.1</td>
565 <td>39939</td>
566 <td>410</td>
567 <td>0.0103</td>
568 <td>0.1008</td>
569 </tr>
570 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
571 <td>GL000202.1</td>
572 <td>40103</td>
573 <td>423</td>
574 <td>0.0105</td>
575 <td>0.1417</td>
576 </tr>
577 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
578 <td>GL000234.1</td>
579 <td>40531</td>
580 <td>733</td>
581 <td>0.0181</td>
582 <td>0.1675</td>
583 </tr>
584 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
585 <td>GL000232.1</td>
586 <td>40652</td>
587 <td>543</td>
588 <td>0.0134</td>
589 <td>0.1194</td>
590 </tr>
591 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
592 <td>GL000206.1</td>
593 <td>41001</td>
594 <td>0</td>
595 <td>0</td>
596 <td>0</td>
597 </tr>
598 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
599 <td>GL000240.1</td>
600 <td>41933</td>
601 <td>475</td>
602 <td>0.0113</td>
603 <td>0.1056</td>
604 </tr>
605 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
606 <td>GL000236.1</td>
607 <td>41934</td>
608 <td>924</td>
609 <td>0.022</td>
610 <td>0.1466</td>
611 </tr>
612 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
613 <td>GL000241.1</td>
614 <td>42152</td>
615 <td>930</td>
616 <td>0.0221</td>
617 <td>0.1716</td>
618 </tr>
619 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
620 <td>GL000243.1</td>
621 <td>43341</td>
622 <td>110</td>
623 <td>0.0025</td>
624 <td>0.0503</td>
625 </tr>
626 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
627 <td>GL000242.1</td>
628 <td>43523</td>
629 <td>444</td>
630 <td>0.0102</td>
631 <td>0.1005</td>
632 </tr>
633 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
634 <td>GL000230.1</td>
635 <td>43691</td>
636 <td>939</td>
637 <td>0.0215</td>
638 <td>0.1544</td>
639 </tr>
640 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
641 <td>GL000237.1</td>
642 <td>45867</td>
643 <td>852</td>
644 <td>0.0186</td>
645 <td>0.135</td>
646 </tr>
647 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
648 <td>GL000233.1</td>
649 <td>45941</td>
650 <td>0</td>
651 <td>0</td>
652 <td>0</td>
653 </tr>
654 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
655 <td>GL000204.1</td>
656 <td>81310</td>
657 <td>1345</td>
658 <td>0.0165</td>
659 <td>0.1549</td>
660 </tr>
661 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
662 <td>GL000198.1</td>
663 <td>90085</td>
664 <td>1750</td>
665 <td>0.0194</td>
666 <td>0.1441</td>
667 </tr>
668 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
669 <td>GL000208.1</td>
670 <td>92689</td>
671 <td>3998</td>
672 <td>0.0431</td>
673 <td>0.2697</td>
674 </tr>
675 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
676 <td>GL000191.1</td>
677 <td>106433</td>
678 <td>0</td>
679 <td>0</td>
680 <td>0</td>
681 </tr>
682 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
683 <td>GL000227.1</td>
684 <td>128374</td>
685 <td>476</td>
686 <td>0.0037</td>
687 <td>0.0608</td>
688 </tr>
689 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
690 <td>GL000228.1</td>
691 <td>129120</td>
692 <td>4339</td>
693 <td>0.0336</td>
694 <td>0.3105</td>
695 </tr>
696 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
697 <td>GL000214.1</td>
698 <td>137718</td>
699 <td>2220</td>
700 <td>0.0161</td>
701 <td>0.1342</td>
702 </tr>
703 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
704 <td>GL000221.1</td>
705 <td>155397</td>
706 <td>2809</td>
707 <td>0.0181</td>
708 <td>0.174</td>
709 </tr>
710 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
711 <td>GL000209.1</td>
712 <td>159169</td>
713 <td>463</td>
714 <td>0.0029</td>
715 <td>0.0574</td>
716 </tr>
717 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
718 <td>GL000218.1</td>
719 <td>161147</td>
720 <td>1369</td>
721 <td>0.0085</td>
722 <td>0.1116</td>
723 </tr>
724 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
725 <td>GL000220.1</td>
726 <td>161802</td>
727 <td>40235</td>
728 <td>0.2487</td>
729 <td>0.6522</td>
730 </tr>
731 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
732 <td>GL000213.1</td>
733 <td>164239</td>
734 <td>490</td>
735 <td>0.003</td>
736 <td>0.0545</td>
737 </tr>
738 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
739 <td>GL000211.1</td>
740 <td>166566</td>
741 <td>384</td>
742 <td>0.0023</td>
743 <td>0.0679</td>
744 </tr>
745 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
746 <td>GL000199.1</td>
747 <td>169874</td>
748 <td>21154</td>
749 <td>0.1245</td>
750 <td>0.5192</td>
751 </tr>
752 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
753 <td>GL000217.1</td>
754 <td>172149</td>
755 <td>2403</td>
756 <td>0.014</td>
757 <td>0.1307</td>
758 </tr>
759 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
760 <td>GL000216.1</td>
761 <td>172294</td>
762 <td>13420</td>
763 <td>0.0779</td>
764 <td>0.4454</td>
765 </tr>
766 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
767 <td>GL000215.1</td>
768 <td>172545</td>
769 <td>960</td>
770 <td>0.0056</td>
771 <td>0.0995</td>
772 </tr>
773 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
774 <td>GL000205.1</td>
775 <td>174588</td>
776 <td>1778</td>
777 <td>0.0102</td>
778 <td>0.1251</td>
779 </tr>
780 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
781 <td>GL000219.1</td>
782 <td>179198</td>
783 <td>1205</td>
784 <td>0.0067</td>
785 <td>0.092</td>
786 </tr>
787 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
788 <td>GL000224.1</td>
789 <td>179693</td>
790 <td>2523</td>
791 <td>0.014</td>
792 <td>0.1396</td>
793 </tr>
794 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
795 <td>GL000223.1</td>
796 <td>180455</td>
797 <td>622</td>
798 <td>0.0034</td>
799 <td>0.0586</td>
800 </tr>
801 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
802 <td>GL000195.1</td>
803 <td>182896</td>
804 <td>2173</td>
805 <td>0.0119</td>
806 <td>0.1236</td>
807 </tr>
808 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
809 <td>GL000212.1</td>
810 <td>186858</td>
811 <td>1274</td>
812 <td>0.0068</td>
813 <td>0.1243</td>
814 </tr>
815 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
816 <td>GL000222.1</td>
817 <td>186861</td>
818 <td>437</td>
819 <td>0.0023</td>
820 <td>0.0482</td>
821 </tr>
822 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
823 <td>GL000200.1</td>
824 <td>187035</td>
825 <td>370</td>
826 <td>0.002</td>
827 <td>0.0629</td>
828 </tr>
829 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
830 <td>GL000193.1</td>
831 <td>189789</td>
832 <td>3642</td>
833 <td>0.0192</td>
834 <td>0.1547</td>
835 </tr>
836 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
837 <td>GL000194.1</td>
838 <td>191469</td>
839 <td>1260</td>
840 <td>0.0066</td>
841 <td>0.0909</td>
842 </tr>
843 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
844 <td>GL000225.1</td>
845 <td>211173</td>
846 <td>10094</td>
847 <td>0.0478</td>
848 <td>0.2717</td>
849 </tr>
850 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
851 <td>GL000192.1</td>
852 <td>547496</td>
853 <td>3452</td>
854 <td>0.0063</td>
855 <td>0.0849</td>
856 </tr>
857 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
858 <td>NC_007605</td>
859 <td>171823</td>
860 <td>12864</td>
861 <td>0.0749</td>
862 <td>0.298</td>
863 </tr>
864 </table>
865 </div>
866
867 </div>
868 </div> <!-- summary section -->
869
870
871
872 <div class=section>
873
874 <h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
875
876 <div><img width=100% src="images_qualimapReport/genome_coverage_across_reference.png"></div>
877
878 </div><!-- graph section -->
879
880
881 <div class=section>
882
883 <h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
884
885 <div><img width=100% src="images_qualimapReport/genome_coverage_histogram.png"></div>
886
887 </div><!-- graph section -->
888
889
890 <div class=section>
891
892 <h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
893
894 <div><img width=100% src="images_qualimapReport/genome_coverage_0to50_histogram.png"></div>
895
896 </div><!-- graph section -->
897
898
899 <div class=section>
900
901 <h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline">&nbsp;</a></h2>
902
903 <div><img width=100% src="images_qualimapReport/genome_coverage_quotes.png"></div>
904
905 </div><!-- graph section -->
906
907
908 <div class=section>
909
910 <h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
911
912 <div><img width=100% src="images_qualimapReport/genome_uniq_read_starts_histogram.png"></div>
913
914 </div><!-- graph section -->
915
916
917 <div class=section>
918
919 <h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline">&nbsp;</a></h2>
920
921 <div><img width=100% src="images_qualimapReport/genome_reads_content_per_read_position.png"></div>
922
923 </div><!-- graph section -->
924
925
926 <div class=section>
927
928 <h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline">&nbsp;</a></h2>
929
930 <div><img width=100% src="images_qualimapReport/genome_gc_content_per_window.png"></div>
931
932 </div><!-- graph section -->
933
934
935 <div class=section>
936
937 <h2>Mapped Reads Clipping Profile<a class="headerlink" name="genome_reads_clipping_profile.png" title="Permalink to this headline">&nbsp;</a></h2>
938
939 <div><img width=100% src="images_qualimapReport/genome_reads_clipping_profile.png"></div>
940
941 </div><!-- graph section -->
942
943
944 <div class=section>
945
946 <h2>Homopolymer Indels<a class="headerlink" name="genome_homopolymer_indels" title="Permalink to this headline">&nbsp;</a></h2>
947
948 <div><img width=100% src="images_qualimapReport/genome_homopolymer_indels.png"></div>
949
950 </div><!-- graph section -->
951
952
953 <div class=section>
954
955 <h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
956
957 <div><img width=100% src="images_qualimapReport/genome_mapping_quality_across_reference.png"></div>
958
959 </div><!-- graph section -->
960
961
962 <div class=section>
963
964 <h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
965
966 <div><img width=100% src="images_qualimapReport/genome_mapping_quality_histogram.png"></div>
967
968 </div><!-- graph section -->
969
970
971 <div class=section>
972
973 <h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
974
975 <div><img width=100% src="images_qualimapReport/genome_insert_size_across_reference.png"></div>
976
977 </div><!-- graph section -->
978
979
980 <div class=section>
981
982 <h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
983
984 <div><img width=100% src="images_qualimapReport/genome_insert_size_histogram.png"></div>
985
986 </div><!-- graph section -->
987
988
989 </div>
990
991 </div>
992
993 </div>
994
995 </div>
996
997
998 <div class="sidebar">
999 <h3>Contents</h3>
1000 <li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
1001 <li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
1002 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
1003 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
1004 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
1005 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
1006 <li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
1007 <li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
1008 <li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
1009 <li class="toctree-l1"><a class="reference internal" href="#genome_reads_clipping_profile.png">Mapped Reads Clipping Profile</a></li>
1010 <li class="toctree-l1"><a class="reference internal" href="#genome_homopolymer_indels">Homopolymer Indels</a></li>
1011 <li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
1012 <li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
1013 <li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
1014 <li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
1015 </div> <!-- sidebar -->
1016
1017 <div class="clearer"></div>
1018 </div>
1019
1020 </div>
1021
1022
1023 <div class="footer-wrapper">
1024 <div class="footer">
1025 <div class="left">
1026 <div class="footer">
1027 2018/07/26 13:34:53
1028 </div>
1029 </div>
1030 <div class="right">
1031 <div class="footer">
1032 Generated by QualiMap v.2.2
1033 </div
1034 </div>
1035 <div class="clearer"></div>
1036 </div> <!-- footer -->
1037 </div>
1038 </body>