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comparison test-data/test_stats/qualimapReport.html @ 30:418ee04dd1b2 draft

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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:40:19 -0400
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29:71af3fbe85be 30:418ee04dd1b2
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 ../qualimap2/test-data/test.bam -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 16:33:35 EDT 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>../qualimap2/test-data/test.bam</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>Secondary alignments</td>
134 <td class=column2>0</td>
135 </tr>
136 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
137 <td class=column1>Supplementary alignments</td>
138 <td class=column2>1,169 / 1.91%</td>
139 </tr>
140 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
141 <td class=column1>Read min/max/mean length</td>
142 <td class=column2>250 / 250 / 250</td>
143 </tr>
144 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
145 <td class=column1>Duplicated reads (flagged)</td>
146 <td class=column2>48 / 0.08%</td>
147 </tr>
148 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
149 <td class=column1>Clipped reads</td>
150 <td class=column2>33,606 / 54.94%</td>
151 </tr>
152 </table>
153 </div>
154
155
156 <div class=table-summary>
157 <h3>ACGT Content</h3>
158 <table class="summary hovertable">
159 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
160 <td class=column1>Number/percentage of A's</td>
161 <td class=column2>3,912,917 / 29.53%</td>
162 </tr>
163 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
164 <td class=column1>Number/percentage of C's</td>
165 <td class=column2>2,699,395 / 20.37%</td>
166 </tr>
167 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
168 <td class=column1>Number/percentage of T's</td>
169 <td class=column2>3,942,019 / 29.75%</td>
170 </tr>
171 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
172 <td class=column1>Number/percentage of G's</td>
173 <td class=column2>2,694,640 / 20.34%</td>
174 </tr>
175 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
176 <td class=column1>Number/percentage of N's</td>
177 <td class=column2>14,397 / 0.11%</td>
178 </tr>
179 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
180 <td class=column1>GC Percentage</td>
181 <td class=column2>40.71%</td>
182 </tr>
183 </table>
184 </div>
185
186
187 <div class=table-summary>
188 <h3>Coverage</h3>
189 <table class="summary hovertable">
190 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
191 <td class=column1>Mean</td>
192 <td class=column2>0.0043</td>
193 </tr>
194 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
195 <td class=column1>Standard Deviation</td>
196 <td class=column2>0.0869</td>
197 </tr>
198 </table>
199 </div>
200
201
202 <div class=table-summary>
203 <h3>Mapping Quality</h3>
204 <table class="summary hovertable">
205 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
206 <td class=column1>Mean Mapping Quality</td>
207 <td class=column2>49.97</td>
208 </tr>
209 </table>
210 </div>
211
212
213 <div class=table-summary>
214 <h3>Insert size</h3>
215 <table class="summary hovertable">
216 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
217 <td class=column1>Mean</td>
218 <td class=column2>75,226.79</td>
219 </tr>
220 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
221 <td class=column1>Standard Deviation</td>
222 <td class=column2>2,849,315.96</td>
223 </tr>
224 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
225 <td class=column1>P25/Median/P75</td>
226 <td class=column2>339 / 427 / 535</td>
227 </tr>
228 </table>
229 </div>
230
231
232 <div class=table-summary>
233 <h3>Mismatches and indels</h3>
234 <table class="summary hovertable">
235 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
236 <td class=column1>General error rate</td>
237 <td class=column2>1.49%</td>
238 </tr>
239 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
240 <td class=column1>Mismatches</td>
241 <td class=column2>190,508</td>
242 </tr>
243 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
244 <td class=column1>Insertions</td>
245 <td class=column2>2,279</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 insertion</td>
249 <td class=column2>3.3%</td>
250 </tr>
251 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
252 <td class=column1>Deletions</td>
253 <td class=column2>2,316</td>
254 </tr>
255 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
256 <td class=column1>Mapped reads with at least one deletion</td>
257 <td class=column2>3.41%</td>
258 </tr>
259 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
260 <td class=column1>Homopolymer indels</td>
261 <td class=column2>50.79%</td>
262 </tr>
263 </table>
264 </div>
265
266
267 <div class=table-summary>
268 <h3>Chromosome stats</h3>
269 <table class="summary hovertable">
270 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
271 <td><b>Name</b></td>
272 <td><b>Length</b></td>
273 <td><b>Mapped bases</b></td>
274 <td><b>Mean coverage</b></td>
275 <td><b>Standard deviation</b></td>
276 </tr>
277 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
278 <td>1</td>
279 <td>249250621</td>
280 <td>1063202</td>
281 <td>0.0043</td>
282 <td>0.1147</td>
283 </tr>
284 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
285 <td>2</td>
286 <td>243199373</td>
287 <td>1091086</td>
288 <td>0.0045</td>
289 <td>0.082</td>
290 </tr>
291 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
292 <td>3</td>
293 <td>198022430</td>
294 <td>906302</td>
295 <td>0.0046</td>
296 <td>0.0765</td>
297 </tr>
298 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
299 <td>4</td>
300 <td>191154276</td>
301 <td>899976</td>
302 <td>0.0047</td>
303 <td>0.088</td>
304 </tr>
305 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
306 <td>5</td>
307 <td>180915260</td>
308 <td>759318</td>
309 <td>0.0042</td>
310 <td>0.0739</td>
311 </tr>
312 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
313 <td>6</td>
314 <td>171115067</td>
315 <td>734471</td>
316 <td>0.0043</td>
317 <td>0.0752</td>
318 </tr>
319 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
320 <td>7</td>
321 <td>159138663</td>
322 <td>654165</td>
323 <td>0.0041</td>
324 <td>0.0773</td>
325 </tr>
326 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
327 <td>8</td>
328 <td>146364022</td>
329 <td>676934</td>
330 <td>0.0046</td>
331 <td>0.1184</td>
332 </tr>
333 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
334 <td>9</td>
335 <td>141213431</td>
336 <td>525097</td>
337 <td>0.0037</td>
338 <td>0.0766</td>
339 </tr>
340 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
341 <td>10</td>
342 <td>135534747</td>
343 <td>724777</td>
344 <td>0.0053</td>
345 <td>0.1311</td>
346 </tr>
347 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
348 <td>11</td>
349 <td>135006516</td>
350 <td>589118</td>
351 <td>0.0044</td>
352 <td>0.082</td>
353 </tr>
354 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
355 <td>12</td>
356 <td>133851895</td>
357 <td>581268</td>
358 <td>0.0043</td>
359 <td>0.0745</td>
360 </tr>
361 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
362 <td>13</td>
363 <td>115169878</td>
364 <td>424915</td>
365 <td>0.0037</td>
366 <td>0.0689</td>
367 </tr>
368 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
369 <td>14</td>
370 <td>107349540</td>
371 <td>385363</td>
372 <td>0.0036</td>
373 <td>0.068</td>
374 </tr>
375 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
376 <td>15</td>
377 <td>102531392</td>
378 <td>361006</td>
379 <td>0.0035</td>
380 <td>0.0671</td>
381 </tr>
382 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
383 <td>16</td>
384 <td>90354753</td>
385 <td>405846</td>
386 <td>0.0045</td>
387 <td>0.0833</td>
388 </tr>
389 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
390 <td>17</td>
391 <td>81195210</td>
392 <td>351366</td>
393 <td>0.0043</td>
394 <td>0.0765</td>
395 </tr>
396 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
397 <td>18</td>
398 <td>78077248</td>
399 <td>355035</td>
400 <td>0.0045</td>
401 <td>0.0817</td>
402 </tr>
403 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
404 <td>19</td>
405 <td>59128983</td>
406 <td>263166</td>
407 <td>0.0045</td>
408 <td>0.0888</td>
409 </tr>
410 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
411 <td>20</td>
412 <td>63025520</td>
413 <td>262814</td>
414 <td>0.0042</td>
415 <td>0.0805</td>
416 </tr>
417 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
418 <td>21</td>
419 <td>48129895</td>
420 <td>179259</td>
421 <td>0.0037</td>
422 <td>0.0748</td>
423 </tr>
424 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
425 <td>22</td>
426 <td>51304566</td>
427 <td>150578</td>
428 <td>0.0029</td>
429 <td>0.0612</td>
430 </tr>
431 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
432 <td>X</td>
433 <td>155270560</td>
434 <td>669025</td>
435 <td>0.0043</td>
436 <td>0.0753</td>
437 </tr>
438 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
439 <td>Y</td>
440 <td>59373566</td>
441 <td>28998</td>
442 <td>0.0005</td>
443 <td>0.049</td>
444 </tr>
445 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
446 <td>MT</td>
447 <td>16569</td>
448 <td>56251</td>
449 <td>3.395</td>
450 <td>2.0903</td>
451 </tr>
452 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
453 <td>GL000207.1</td>
454 <td>4262</td>
455 <td>0</td>
456 <td>0</td>
457 <td>0</td>
458 </tr>
459 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
460 <td>GL000226.1</td>
461 <td>15008</td>
462 <td>21953</td>
463 <td>1.4628</td>
464 <td>1.7817</td>
465 </tr>
466 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
467 <td>GL000229.1</td>
468 <td>19913</td>
469 <td>0</td>
470 <td>0</td>
471 <td>0</td>
472 </tr>
473 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
474 <td>GL000231.1</td>
475 <td>27386</td>
476 <td>1169</td>
477 <td>0.0427</td>
478 <td>0.2278</td>
479 </tr>
480 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
481 <td>GL000210.1</td>
482 <td>27682</td>
483 <td>0</td>
484 <td>0</td>
485 <td>0</td>
486 </tr>
487 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
488 <td>GL000239.1</td>
489 <td>33824</td>
490 <td>0</td>
491 <td>0</td>
492 <td>0</td>
493 </tr>
494 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
495 <td>GL000235.1</td>
496 <td>34474</td>
497 <td>0</td>
498 <td>0</td>
499 <td>0</td>
500 </tr>
501 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
502 <td>GL000201.1</td>
503 <td>36148</td>
504 <td>0</td>
505 <td>0</td>
506 <td>0</td>
507 </tr>
508 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
509 <td>GL000247.1</td>
510 <td>36422</td>
511 <td>0</td>
512 <td>0</td>
513 <td>0</td>
514 </tr>
515 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
516 <td>GL000245.1</td>
517 <td>36651</td>
518 <td>481</td>
519 <td>0.0131</td>
520 <td>0.1138</td>
521 </tr>
522 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
523 <td>GL000197.1</td>
524 <td>37175</td>
525 <td>0</td>
526 <td>0</td>
527 <td>0</td>
528 </tr>
529 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
530 <td>GL000203.1</td>
531 <td>37498</td>
532 <td>459</td>
533 <td>0.0122</td>
534 <td>0.1178</td>
535 </tr>
536 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
537 <td>GL000246.1</td>
538 <td>38154</td>
539 <td>0</td>
540 <td>0</td>
541 <td>0</td>
542 </tr>
543 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
544 <td>GL000249.1</td>
545 <td>38502</td>
546 <td>483</td>
547 <td>0.0125</td>
548 <td>0.1113</td>
549 </tr>
550 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
551 <td>GL000196.1</td>
552 <td>38914</td>
553 <td>0</td>
554 <td>0</td>
555 <td>0</td>
556 </tr>
557 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
558 <td>GL000248.1</td>
559 <td>39786</td>
560 <td>456</td>
561 <td>0.0115</td>
562 <td>0.1064</td>
563 </tr>
564 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
565 <td>GL000244.1</td>
566 <td>39929</td>
567 <td>0</td>
568 <td>0</td>
569 <td>0</td>
570 </tr>
571 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
572 <td>GL000238.1</td>
573 <td>39939</td>
574 <td>410</td>
575 <td>0.0103</td>
576 <td>0.1008</td>
577 </tr>
578 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
579 <td>GL000202.1</td>
580 <td>40103</td>
581 <td>423</td>
582 <td>0.0105</td>
583 <td>0.1417</td>
584 </tr>
585 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
586 <td>GL000234.1</td>
587 <td>40531</td>
588 <td>733</td>
589 <td>0.0181</td>
590 <td>0.1675</td>
591 </tr>
592 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
593 <td>GL000232.1</td>
594 <td>40652</td>
595 <td>543</td>
596 <td>0.0134</td>
597 <td>0.1194</td>
598 </tr>
599 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
600 <td>GL000206.1</td>
601 <td>41001</td>
602 <td>0</td>
603 <td>0</td>
604 <td>0</td>
605 </tr>
606 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
607 <td>GL000240.1</td>
608 <td>41933</td>
609 <td>475</td>
610 <td>0.0113</td>
611 <td>0.1056</td>
612 </tr>
613 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
614 <td>GL000236.1</td>
615 <td>41934</td>
616 <td>924</td>
617 <td>0.022</td>
618 <td>0.1466</td>
619 </tr>
620 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
621 <td>GL000241.1</td>
622 <td>42152</td>
623 <td>930</td>
624 <td>0.0221</td>
625 <td>0.1716</td>
626 </tr>
627 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
628 <td>GL000243.1</td>
629 <td>43341</td>
630 <td>110</td>
631 <td>0.0025</td>
632 <td>0.0503</td>
633 </tr>
634 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
635 <td>GL000242.1</td>
636 <td>43523</td>
637 <td>444</td>
638 <td>0.0102</td>
639 <td>0.1005</td>
640 </tr>
641 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
642 <td>GL000230.1</td>
643 <td>43691</td>
644 <td>939</td>
645 <td>0.0215</td>
646 <td>0.1544</td>
647 </tr>
648 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
649 <td>GL000237.1</td>
650 <td>45867</td>
651 <td>852</td>
652 <td>0.0186</td>
653 <td>0.135</td>
654 </tr>
655 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
656 <td>GL000233.1</td>
657 <td>45941</td>
658 <td>0</td>
659 <td>0</td>
660 <td>0</td>
661 </tr>
662 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
663 <td>GL000204.1</td>
664 <td>81310</td>
665 <td>1345</td>
666 <td>0.0165</td>
667 <td>0.1549</td>
668 </tr>
669 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
670 <td>GL000198.1</td>
671 <td>90085</td>
672 <td>1750</td>
673 <td>0.0194</td>
674 <td>0.1441</td>
675 </tr>
676 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
677 <td>GL000208.1</td>
678 <td>92689</td>
679 <td>3998</td>
680 <td>0.0431</td>
681 <td>0.2697</td>
682 </tr>
683 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
684 <td>GL000191.1</td>
685 <td>106433</td>
686 <td>0</td>
687 <td>0</td>
688 <td>0</td>
689 </tr>
690 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
691 <td>GL000227.1</td>
692 <td>128374</td>
693 <td>476</td>
694 <td>0.0037</td>
695 <td>0.0608</td>
696 </tr>
697 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
698 <td>GL000228.1</td>
699 <td>129120</td>
700 <td>4339</td>
701 <td>0.0336</td>
702 <td>0.3105</td>
703 </tr>
704 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
705 <td>GL000214.1</td>
706 <td>137718</td>
707 <td>2220</td>
708 <td>0.0161</td>
709 <td>0.1342</td>
710 </tr>
711 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
712 <td>GL000221.1</td>
713 <td>155397</td>
714 <td>2809</td>
715 <td>0.0181</td>
716 <td>0.174</td>
717 </tr>
718 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
719 <td>GL000209.1</td>
720 <td>159169</td>
721 <td>463</td>
722 <td>0.0029</td>
723 <td>0.0574</td>
724 </tr>
725 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
726 <td>GL000218.1</td>
727 <td>161147</td>
728 <td>1369</td>
729 <td>0.0085</td>
730 <td>0.1116</td>
731 </tr>
732 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
733 <td>GL000220.1</td>
734 <td>161802</td>
735 <td>40235</td>
736 <td>0.2487</td>
737 <td>0.6522</td>
738 </tr>
739 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
740 <td>GL000213.1</td>
741 <td>164239</td>
742 <td>490</td>
743 <td>0.003</td>
744 <td>0.0545</td>
745 </tr>
746 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
747 <td>GL000211.1</td>
748 <td>166566</td>
749 <td>384</td>
750 <td>0.0023</td>
751 <td>0.0679</td>
752 </tr>
753 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
754 <td>GL000199.1</td>
755 <td>169874</td>
756 <td>21154</td>
757 <td>0.1245</td>
758 <td>0.5192</td>
759 </tr>
760 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
761 <td>GL000217.1</td>
762 <td>172149</td>
763 <td>2403</td>
764 <td>0.014</td>
765 <td>0.1307</td>
766 </tr>
767 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
768 <td>GL000216.1</td>
769 <td>172294</td>
770 <td>13420</td>
771 <td>0.0779</td>
772 <td>0.4454</td>
773 </tr>
774 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
775 <td>GL000215.1</td>
776 <td>172545</td>
777 <td>960</td>
778 <td>0.0056</td>
779 <td>0.0995</td>
780 </tr>
781 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
782 <td>GL000205.1</td>
783 <td>174588</td>
784 <td>1778</td>
785 <td>0.0102</td>
786 <td>0.1251</td>
787 </tr>
788 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
789 <td>GL000219.1</td>
790 <td>179198</td>
791 <td>1205</td>
792 <td>0.0067</td>
793 <td>0.092</td>
794 </tr>
795 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
796 <td>GL000224.1</td>
797 <td>179693</td>
798 <td>2523</td>
799 <td>0.014</td>
800 <td>0.1396</td>
801 </tr>
802 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
803 <td>GL000223.1</td>
804 <td>180455</td>
805 <td>622</td>
806 <td>0.0034</td>
807 <td>0.0586</td>
808 </tr>
809 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
810 <td>GL000195.1</td>
811 <td>182896</td>
812 <td>2173</td>
813 <td>0.0119</td>
814 <td>0.1236</td>
815 </tr>
816 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
817 <td>GL000212.1</td>
818 <td>186858</td>
819 <td>1274</td>
820 <td>0.0068</td>
821 <td>0.1243</td>
822 </tr>
823 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
824 <td>GL000222.1</td>
825 <td>186861</td>
826 <td>437</td>
827 <td>0.0023</td>
828 <td>0.0482</td>
829 </tr>
830 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
831 <td>GL000200.1</td>
832 <td>187035</td>
833 <td>370</td>
834 <td>0.002</td>
835 <td>0.0629</td>
836 </tr>
837 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
838 <td>GL000193.1</td>
839 <td>189789</td>
840 <td>3642</td>
841 <td>0.0192</td>
842 <td>0.1547</td>
843 </tr>
844 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
845 <td>GL000194.1</td>
846 <td>191469</td>
847 <td>1260</td>
848 <td>0.0066</td>
849 <td>0.0909</td>
850 </tr>
851 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
852 <td>GL000225.1</td>
853 <td>211173</td>
854 <td>10094</td>
855 <td>0.0478</td>
856 <td>0.2717</td>
857 </tr>
858 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
859 <td>GL000192.1</td>
860 <td>547496</td>
861 <td>3452</td>
862 <td>0.0063</td>
863 <td>0.0849</td>
864 </tr>
865 <tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
866 <td>NC_007605</td>
867 <td>171823</td>
868 <td>12864</td>
869 <td>0.0749</td>
870 <td>0.298</td>
871 </tr>
872 </table>
873 </div>
874
875 </div>
876 </div> <!-- summary section -->
877
878
879
880 <div class=section>
881
882 <h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
883
884 <div><img width=100% src="images_qualimapReport/genome_coverage_across_reference.png"></div>
885
886 </div><!-- graph section -->
887
888
889 <div class=section>
890
891 <h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
892
893 <div><img width=100% src="images_qualimapReport/genome_coverage_histogram.png"></div>
894
895 </div><!-- graph section -->
896
897
898 <div class=section>
899
900 <h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
901
902 <div><img width=100% src="images_qualimapReport/genome_coverage_0to50_histogram.png"></div>
903
904 </div><!-- graph section -->
905
906
907 <div class=section>
908
909 <h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline">&nbsp;</a></h2>
910
911 <div><img width=100% src="images_qualimapReport/genome_coverage_quotes.png"></div>
912
913 </div><!-- graph section -->
914
915
916 <div class=section>
917
918 <h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
919
920 <div><img width=100% src="images_qualimapReport/genome_uniq_read_starts_histogram.png"></div>
921
922 </div><!-- graph section -->
923
924
925 <div class=section>
926
927 <h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline">&nbsp;</a></h2>
928
929 <div><img width=100% src="images_qualimapReport/genome_reads_content_per_read_position.png"></div>
930
931 </div><!-- graph section -->
932
933
934 <div class=section>
935
936 <h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline">&nbsp;</a></h2>
937
938 <div><img width=100% src="images_qualimapReport/genome_gc_content_per_window.png"></div>
939
940 </div><!-- graph section -->
941
942
943 <div class=section>
944
945 <h2>Mapped Reads Clipping Profile<a class="headerlink" name="genome_reads_clipping_profile.png" title="Permalink to this headline">&nbsp;</a></h2>
946
947 <div><img width=100% src="images_qualimapReport/genome_reads_clipping_profile.png"></div>
948
949 </div><!-- graph section -->
950
951
952 <div class=section>
953
954 <h2>Homopolymer Indels<a class="headerlink" name="genome_homopolymer_indels" title="Permalink to this headline">&nbsp;</a></h2>
955
956 <div><img width=100% src="images_qualimapReport/genome_homopolymer_indels.png"></div>
957
958 </div><!-- graph section -->
959
960
961 <div class=section>
962
963 <h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
964
965 <div><img width=100% src="images_qualimapReport/genome_mapping_quality_across_reference.png"></div>
966
967 </div><!-- graph section -->
968
969
970 <div class=section>
971
972 <h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
973
974 <div><img width=100% src="images_qualimapReport/genome_mapping_quality_histogram.png"></div>
975
976 </div><!-- graph section -->
977
978
979 <div class=section>
980
981 <h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>
982
983 <div><img width=100% src="images_qualimapReport/genome_insert_size_across_reference.png"></div>
984
985 </div><!-- graph section -->
986
987
988 <div class=section>
989
990 <h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>
991
992 <div><img width=100% src="images_qualimapReport/genome_insert_size_histogram.png"></div>
993
994 </div><!-- graph section -->
995
996
997 </div>
998
999 </div>
1000
1001 </div>
1002
1003 </div>
1004
1005
1006 <div class="sidebar">
1007 <h3>Contents</h3>
1008 <li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
1009 <li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
1010 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
1011 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
1012 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
1013 <li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
1014 <li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
1015 <li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
1016 <li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
1017 <li class="toctree-l1"><a class="reference internal" href="#genome_reads_clipping_profile.png">Mapped Reads Clipping Profile</a></li>
1018 <li class="toctree-l1"><a class="reference internal" href="#genome_homopolymer_indels">Homopolymer Indels</a></li>
1019 <li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
1020 <li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
1021 <li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
1022 <li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
1023 </div> <!-- sidebar -->
1024
1025 <div class="clearer"></div>
1026 </div>
1027
1028 </div>
1029
1030
1031 <div class="footer-wrapper">
1032 <div class="footer">
1033 <div class="left">
1034 <div class="footer">
1035 2018/07/26 16:33:36
1036 </div>
1037 </div>
1038 <div class="right">
1039 <div class="footer">
1040 Generated by QualiMap v.2.2.2-dev
1041 </div
1042 </div>
1043 <div class="clearer"></div>
1044 </div> <!-- footer -->
1045 </div>
1046 </body>