TABLE 4.
H. influenzae genome coverage breadth and depth with Oxford Nanopore; total and H. inf specific reads and bases in HI+ samples shown with coverage breadth (percentage of reference sequences covered), average coverage depth (at positions with ≥1 read) and number of positions on the H. influenzae genome with 1/5/10 read depth
| PID | Bacterial reads | H. inf reads | % H. inf/bacterial reads | Bacterial bases | H. inf bases | % H. inf/bacterial bases | Legth of H. inf reference genome (bases) | Coverage breadth H. inf genome | Avg coverage depth |
H. inf genome positions with: |
||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 read depth | 5 reads depth | 10 reads depth | ||||||||||
| 1054 | 88101 | 82374 | 93.5 | 4.97E + 08 | 4.85E + 08 | 97.7 | 1.83E + 06 | 94.2 | 243.3 | 1.72E + 06 | 1.71E + 06 | 1.70E + 06 |
| 278 | 28460 | 24609 | 86.5 | 1.14E + 08 | 1.12E + 08 | 97.9 | 1.83E + 06 | 93.4 | 53.6 | 1.71E + 06 | 1.70E + 06 | 1.69E + 06 |
| 133 | 6054 | 4031 | 66.6 | 2.43E + 07 | 2.16E + 07 | 89.1 | 1.83E + 06 | 92.7 | 10.1 | 1.70E + 06 | 1.63E + 06 | 7.48E + 05 |
| 297 | 9228 | 6142 | 66.6 | 4.32E + 07 | 3.52E + 07 | 81.6 | 1.83E + 06 | 92.9 | 17.5 | 1.70E + 06 | 1.69E + 06 | 1.60E + 06 |
| 288 | 2775 | 1610 | 58.0 | 9.06E + 06 | 8.47E + 06 | 93.5 | 1.83E + 06 | 90.7 | 4.2 | 1.66E + 06 | 6.80E + 05 | 9.49E + 03 |
| 29 | 2604 | 1226 | 47.1 | 6.97E + 06 | 5.85E + 06 | 83.8 | 1.83E + 06 | 88.9 | 3.2 | 1.63E + 06 | 3.36E + 05 | 1.06E + 02 |
| 214 | 1344 | 230 | 17.1 | 8.53E + 05 | 6.68E + 05 | 78.4 | 1.83E + 06 | 24.2 | 1.3 | 4.43E + 05 | 0.00E + 00 | 0.00E + 00 |
| 1049 | 4632 | 2376 | 51.3 | 1.62E + 07 | 1.21E + 07 | 74.5 | 1.83E + 06 | 92.1 | 6.1 | 1.69E + 06 | 1.21E + 06 | 1.04E + 05 |