Table 1.
Sequencing and coverage statistics for all paired-read libraries
| Library name* | Sequenced pairs | Non-duplicate pairs (%) | Unique, consistently mapped pairs (%) | Median insert size (bp) | Physical coverage (x-fold) | 5 M reads coverage (x-fold) | PCR cycles ** | Relative complexity *** | inconsistent pairs forming clusters | inconsistent inter-chromosomal pairs forming clusters |
|---|---|---|---|---|---|---|---|---|---|---|
| PE |
160 M |
151 M (95%) |
131 M (87%) |
166 |
8.5 |
0.34 |
5 |
>131 M |
9.5% |
2.0% |
| 3 kb |
17.7 M |
16.3 M (92%) |
15.2 M (93%) |
3,208 |
50 |
6 |
14 |
4.6 M |
24.0% |
3.2% |
| 5 kb_a |
11.9 M |
6.0 M (51%) |
5.5 M (92%) |
5,696 |
11 |
10.1 |
18 |
4.7 M |
46.5% |
3.7% |
| 5 kb_b |
16.7 M |
14.7 M (88%) |
14.0 M (95%) |
5,811 |
28 |
10.1 |
13 |
>16.7 M |
47.5% |
4.6% |
| 8 kb_a |
20.8 M |
8.6 M (41%) |
7.8 M (91%) |
8,293 |
25 |
16.2 |
14 |
5.7 M |
58.4% |
6.9% |
| 8 kb_b |
11.8 M |
11.2 M (95%) |
10.6 M (95%) |
8,160 |
34 |
16.2 |
13 |
>11.8 M |
50.6% |
5.5% |
| 15 kb_a |
31.7 M |
1.7 M (5%) |
1.0 M (60%) |
14,561 |
6 |
30.3 |
21 |
0.6 M |
60.8% |
7.6% |
| 15 kb_b |
11.6 M |
1.6 M (14%) |
1.2 M (73%) |
13,556 |
7 |
30.3 |
21 |
0.7 M |
23.2% |
3.2% |
| 20 kb |
13.3 M |
6.7 M (51%) |
5.9 M (87%) |
19,375 |
48 |
40.5 |
14 |
4.9 M |
41.8% |
4.7% |
| 25 kb |
56.9 M |
2.3 M (4%) |
1.1 M (49%) |
25,871 |
11 |
50.6 |
17 |
0.7 M |
51.9% |
5.4% |
| TOTAL | 352.4 M | 220.1 M (62%) | 193.3 M (88%) | 228.5 |
* The _b samples are retrieved from a replicate experiment using an independent DNA isolate from the same animal.
** Number of PCR cycles required to retrieve sufficient library molecules in the final adapter-mediated PCR.
*** Complexity is defined as minimal sequencing depth (in million clones) at which over half of the pairs are clonal.