Table 3:
Comparative analysis among data generated from MinION and MiSeq platforms.
| Relative read proportion | Coverage bias | ||||||
|---|---|---|---|---|---|---|---|
| Genera HM782D | Reference | PCR+MiSeq | PCR+MinION-R9 | PCR+MinION-R9.4 | PCR+MiSeq | PCR+MinION-R9 | PCR+MinION-R9.4 |
| Acinetobacter spp. | 0.050 | 0.019 | 0.046 | 0.032 | –1.42 | –0.12 | –0.62 |
| Actinomyces spp. | 0.050 | 0.010 | 0.001 | 0.003 | –2.36 | –5.36 | –4.02 |
| Bacillus spp. | 0.050 | 0.017 | 0.102 | 0.045 | –1.57 | 1.03 | –0.16 |
| Bacteroides spp. | 0.050 | 0.106 | 0.059 | 0.037 | 1.08 | 0.25 | –0.42 |
| Clostridium spp. | 0.050 | 0.125 | 0.027 | 0.032 | 1.32 | –0.91 | –0.66 |
| Deinococcus spp. | 0.050 | 0.109 | 0.000 | 0.000 | 1.12 | ND | ND |
| Enterococcus spp. | 0.050 | 0.022 | 0.012 | 0.013 | –1.17 | –2.04 | –1.93 |
| Escherichia/Shigella spp. | 0.050 | 0.038 | 0.172 | 0.209 | –0.38 | 1.79 | 2.07 |
| Helicobacter spp. | 0.050 | 0.040 | 0.000 | 0.000 | –0.32 | ND | ND |
| Lactobacillus spp. | 0.050 | 0.065 | 0.051 | 0.068 | 0.38 | 0.03 | 0.45 |
| Listeria spp. | 0.050 | 0.024 | 0.074 | 0.133 | –1.04 | 0.57 | 1.41 |
| Neisseria spp. | 0.050 | 0.099 | 0.064 | 0.056 | 0.98 | 0.36 | 0.17 |
| Propionibacterium spp. | 0.050 | 0.021 | 0.079 | 0.097 | –1.25 | 0.66 | 0.96 |
| Pseudomonas spp. | 0.050 | 0.038 | 0.018 | 0.079 | –0.39 | –1.46 | 0.67 |
| Rhodobacter spp. | 0.050 | 0.013 | 0.002 | 0.004 | –1.91 | –4.36 | –3.51 |
| Staphylococcus spp. | 0.100 | 0.037 | 0.125 | 0.086 | –1.44 | 0.32 | –0.22 |
| Streptococcus spp. | 0.150 | 0.217 | 0.115 | 0.093 | 0.53 | –0.38 | –0.69 |
| Genera D6305 | |||||||
| Bacillus spp. | 0.139 | 0.574 | 0.383 | 0.340 | 2.04 | 1.46 | 1.29 |
| Enterococcus spp. | 0.088 | 0.078 | 0.057 | 0.082 | –0.17 | –0.64 | –0.11 |
| Escherichia/Shigella spp. | 0.113 | 0.035 | 0.167 | 0.137 | –1.67 | 0.56 | 0.28 |
| Lactobacillus spp. | 0.198 | 0.104 | 0.049 | 0.049 | –0.93 | –2.01 | –2.01 |
| Listeria spp. | 0.163 | 0.046 | 0.080 | 0.118 | –1.82 | –1.03 | –0.46 |
| Pseudomonas spp. | 0.058 | 0.060 | 0.038 | 0.039 | 0.05 | –0.62 | –0.56 |
| Salmonella spp. | 0.115 | 0.049 | 0.099 | 0.138 | –1.22 | –0.22 | 0.26 |
| Staphylococcus spp. | 0.126 | 0.051 | 0.094 | 0.095 | –1.30 | –0.42 | –0.41 |
| Average | 0.080 | 0.080 | 0.077 | 0.079 | –0.51 | –0.55 | –0.36 |
| Median | 0.050 | 0.048 | 0.062 | 0.074 | –0.72 | –0.30 | –0.29 |
| Min | 0.050 | 0.010 | 0.000 | 0.000 | –2.36 | –5.36 | –4.02 |
| Max | 0.198 | 0.574 | 0.383 | 0.340 | 2.04 | 1.79 | 2.07 |
| Pearson's Ra (P-value) | – | 0.39 (0.0504) | 0.43 (0.0306) | 0.41 (0.0417) | |||
| Pearson's Rb (P-value) | – | – | 0.73 (0.0001) | 0.64 (0.0005) | |||
aPearson's R calculated from comparisons of R9, R9.4, and MiSeq data with reference proportions, respectively.
bPearson's R calculated from comparisons of R9 and R9.4 data with MiSeq output, respectively.