Table 8 Bacterial genomes reference-based
From: Unified metagenomic method for rapid detection of microorganisms in clinical samples
Sample number | Organisms | Read count | Median read length | Mean read quality | Contigs | Largest contig | Total length | Reference length | Coverage | Coverage %10× | Coverage %15× | Coverage %20× | Coverage %30× |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
56 | S. pyogenes | 291547 | 3312 | 14.4 | 1 | 1.74 | 1.74 | 1.74 | 100.00 | 96.653 | 96.508 | 96.431 | 96.297 |
67 | K. pneumoniae | 10577 | 2115 | 13.52 | 7 | 5.34 | 5.69 | 5.71 | 99.65 | 5.778 | 4.479 | 3.666 | 2.509 |
69 | P. multocida | 18287 | 2861 | 14 | 1 | 2.28 | 2.28 | 2.46 | 92.68 | 87.619 | 73.309 | 48.401 | 9.682 |
70 | B. cenocepacia (H) | 314869 | 2337 | 12.7 | 3 | 3.58 | 7.75 | 7.76 | 99.87 | 69.46 | 63.936 | 59.357 | 51.308 |
72 | S. marcescens (L) | 569552 | 2764 | 13 | 2 | 5.05 | 5.08 | 5.04 | 100.79 | 85.431 | 84.932 | 84.481 | 83.548 |
78 | S. liquacences (not reported) | 244191 | 2199 | 13.5 | 3 | 5.29 | 5.3 | 5.59 | 94.81 | N/A | N/A | N/A | N/A |
85 | K.pneumoniae (H) | 186128 | 3558 | 13.4 | 7 | 5.25 | 5.59 | 5.83 | 95.88 | 91.058 | 90.904 | 90.41 | 88.317 |
87 | P. aeruginosa (H) | 367192 | 2203 | 13.5 | 1 | 6.25 | 6.25 | 6.54 | 95.57 | 81.615 | 78.298 | 75.473 | 70.637 |
90 | K. aerogenes (H) | 19182 | 2150 | 14 | 2 | 5.17 | 5.24 | 5.49 | 95.45 | 21.273 | 5.813 | 2.269 | 0.737 |
90 | E. coli (not reported) | 276158 | 2219 | 14 | 1 | 4.59 | 4.59 | 4.53 | 101.32 | 95.453 | 95.352 | 95.241 | 95.091 |
37 | C. freundii (M) | 57621 | 1516 | 13.5 | 2 | 4.91 | 5.04 | 5.6 | 90.00 | 70.843 | 40.812 | 18.852 | 3.746 |
49 | P. aeruginosa (H) | 115331 | 2786 | 13.5 | 1 | 6.23 | 6.23 | 7.05 | 88.37 | N/A | N/A | N/A | N/A |
P9 | S. pyogenes (M) | 542904 | 2050 | 14 | 1 | 1.74 | 1.74 | 1.74 | 100.00 | 95.67 | 95.623 | 95.586 | 95.532 |
P10 | E. hormaechei (H) | 114305 | 3994 | 14 | 2 | 4.71 | 4.71 | 5.04 | 93.45 | 89.15 | 88.978 | 88.734 | 87.544 |
P10 | S. aureus (H) | 107732 | 3383 | 15 | 1 | 2.81 | 2.81 | 2.86 | 98.25 | 95.768 | 95.741 | 95.722 | 95.454 |
P22 | H. influenzae (not reported) | 150369 | 2390 | 14 | 1 | 1.83 | 1.83 | 1.81 | 101.10 | 90.158 | 89.701 | 89.029 | 87.513 |
P20 | P. mirabilis (not reported) | 380754 | 1613 | 14 | 2 | 4.01 | 4.05 | 4.14 | 97.83 | 92.946 | 92.587 | 92.204 | 91.304 |
P23 | S. pneumoniae (not reported) | 40799 | 2330 | 13.64 | 2 | 2.1 | 2.1 | 1.8 | 116.67 | 83.052 | 77.169 | 67.421 | 49.274 |
