Table 2.
Overview of read numbers obtained for the 48 librairies and the merge value for the 12 samples.
| Name | Rep.* | Raw reads | Clean reads | Identified reads | Viral reads | Coef. of var. %** | Viral reads %*** |
|---|---|---|---|---|---|---|---|
| 2006-D | 1 2 3 4 |
4,506,340 2,402,894 3,606,002 3,206,050 |
688,804 393,000 393,464 312,984 |
387,983 266,782 289,073 120,321 |
361,518 249,453 288,018 119,597 |
40 | |
| Merge | 13,721,286 | 1,788,252 | 1,323,336 | 1,272,409 | 71 | ||
| 2006-G | 1 2 3 4 |
9,541,300 11,217,902 2,966,010 6,423,356 |
2,260,746 1,530,728 356,374 598,924 |
1,488,848 1,274,720 209,670 340,585 |
990,656 1,261,356 208,750 335,904 |
88 | |
| Merge | 30,148,568 | 4,743,756 | 3,699,942 | 3,167,343 | 67 | ||
| 2006-M | 1 2 3 4 |
17,134 47,644,656 14,262,232 76,825,830 |
5,236 4,573,184 1,191,024 7,576,116 |
2,582 4,187,147 930,015 7,053,620 |
2,582 4,173,108 928,085 7,026,021 |
106 | |
| Merge | 138,749,852 | 13,343,538 | 12,436,823 | 12,386,553 | 93 | ||
| 2006-G2 | 1 2 3 4 |
29,093,288 8,137,376 85,435,164 1,565,594 |
4,081,130 680,206 8,064,160 132,970 |
3,522,608 562,770 7,529,846 16,431 |
3,041,567 562,451 7,509,918 14,371 |
123 | |
| Merge | 124,231,422 | 12,953,180 | 11,718,516 | 11,211,954 | 87 | ||
| 2007-P | 1 2 3 4 |
5,774,206 9,458,542 8,181,372 3,455,326 |
92,5,076 919,580 862,832 338,988 |
464,453 620,486 676,385 162,431 |
410,478 611,586 673,825 158,685 |
50 | |
| Merge | 26,869,446 | 3,044,114 | 2,149,086 | 2,061,661 | 68 | ||
| 2009-P | 1 2 3 4 |
3,772,094 4,836,042 372,442 5,450,408 |
698,092 587,498 37,518 448,972 |
374,629 407,026 22,264 209,349 |
213,068 300,583 17,321 180,879 |
67 | |
| Merge | 14,430,986 | 1,770,770 | 1,107,117 | 795,808 | 45 | ||
| 2012-K | 1 2 3 4 |
14,176,218 9,356,070 3,554,214 36,261,558 |
4,587,968 2,572,568 450,022 2,545,060 |
1,060,613 2,110,438 197,616 2,086,422 |
558,029 1,684,264 137,633 2,038,462 |
82 | |
| Merge | 63,348,060 | 10,150,928 | 5,871,134 | 4,810,896 | 47 | ||
| 2014-K2 | 1 2 3 4 |
1,856,764 3,872,212 52,270,136 736,618 |
558,526 588,342 3,846,026 263,830 |
256,651 324,504 3,371,485 20,151 |
98,446 213,169 3,300,670 2,553 |
109 | |
| Merge | 58,735,730 | 5,256,534 | 4,041,606 | 3,686,030 | 70 | ||
| 2014-K1 | 1 2 3 4 |
12,176,666 16,887,440 3,298,316 3,114,878 |
2,336,528 1,544,840 298,646 239,354 |
1,514,188 1,115,033 162,226 128,259 |
984,878 779,709 150,098 118,964 |
87 | |
| Merge | 35,477,300 | 4,418,862 | 3,153,740 | 2,248,319 | 51 | ||
| 2014-K | 1 2 3 4 |
9,137,872 12,253,584 5,421,844 39,869,020 |
1,418,210 1,132,042 447,440 4,487,688 |
877,541 858,364 222,963 3,574,163 |
789,752 850,963 218,749 3,444,980 |
177 | |
| Merge | 66,682,320 | 7,485,152 | 5,957,168 | 5,720,168 | 76 | ||
| 2016-B | 1 2 3 4 |
10,936,716 68,870,930 39,108,178 21,645,010 |
2,801,174 8,652,778 3,875,918 2,476,722 |
1,762,383 7,858,150 3,124,556 2,031,273 |
1,440,351 7,735,805 3,042,426 2,012,830 |
81 | |
| Merge | 140,560,834 | 17,795,292 | 15,290,037 | 14,708,048 | 83 | ||
| 2016-B2 | 1 2 3 4 |
24,749,188 48,291,662 715,534 31,200,266 |
5,210,512 13,195,394 104,526 3,267,994 |
3,080,758 11,603,668 76,346 2,112,003 |
2,350,567 9,160,827 75,782 2,029,485 |
117 | |
| Merge | 104,956,650 | 21,772,204 | 17,266,476 | 14,007,068 | 64 | ||
| Control | 35,160 | 11,458 | 414 | 0 |
*
Data are provided for each replicate (rep.) and for the merge value of all four replicates for each sample (grey line),
**
Coefficient of variation is calculated as the ratio of the standard deviation to the mean ,
***
Percentage of viral reads calculated based on viral reads divided by clean reads, and multiplied by 100.