TABLE 2.
The impact of HMW DNA extraction protocol on proportional read numbers and sequence lengths according to read type (microbial vs. human)
| Qiagen Genomic Tip (GT) | Phenol–chloroform (PC) | Agarose encasement (AE) | ||||
|---|---|---|---|---|---|---|
| GT_1 | GT_2 | PC_1 | PC_2 | AE_1 | AE_2 | |
| All reads | ||||||
| Number of reads | 2,052,300 | 3,681,083 | 2,008,795 | 4,338,575 | 739,186 | 962,065 |
| Sequencing yield (Gbp) | 1.440 | 1.959 | 1.311 | 1.972 | 0.767 | 1.133 |
| Human reads | ||||||
| Number of reads | 1,584,229 | 2,674,013 | 1,664,447 | 3,433,184 | 490,377 | 585,733 |
| % | 77.19 | 72.64 | 82.86 | 79.13 | 66.34 | 60.88 |
| Sequencing yield (Gbp) | 0.908 | 1.199 | 1.026 | 1.536 | 0.405 | 0.463 |
| % | 63.07 | 61.23 | 78.26 | 77.88 | 52.79 | 40.91 |
| Microbial reads | ||||||
| Number of reads | 468,071 | 1,007,070 | 344,348 | 905,391 | 248,809 | 376,332 |
| % | 22.81 | 27.36 | 17.14 | 20.87 | 33.66 | 39.12 |
| Sequencing yield (Gbp) | 0.532 | 0.759 | 0.285 | 0.436 | 0.362 | 0.669 |
| % | 36.93 | 38.77 | 21.74 | 22.12 | 47.21 | 59.09 |