Table 1.
Taxonomic agreement between shotgun and 16S. In the first column, number of unique taxa detected by 16S and shotgun sequencing methods, and shared taxa in absolute and relative frequency with respect to shotgun and 16S. all samples and taxonomic ranks are taken into account. In the second column, the 16S-shotgun agreement is computed per sample. We show the median and range of the shared taxa across all samples, the percentage of common taxa with respect to shotgun and 16S and Cohen’s Kappa agreement coefficient; and Spearman correlation coefficient (rho) median, quartile 1 (Q1) and (Q3)
| Taxonomy level | 16S | Shotgun | Shared | Shared/16S (%) | Shared/shotgun (%) | Shared Median (range) |
Shared/16S(%) Median (range) |
Shared/ shotgun(%) Median (range) |
Rho Median (Q1, Q3) |
Kappa Median (range) |
|---|---|---|---|---|---|---|---|---|---|---|
| Phylum | 15 | 21 | 15 | 100.0 | 71.4 |
8 (4, 12) |
100.0 (100.0, 100.0) |
53.3 (26.7, 80.0) |
0.95 (0.83, 0.99) |
0.73 (0.20, 1) |
| Class | 23 | 33 | 23 | 100.0 | 69.7 |
14 (7, 20) |
100.0 (90.0, 100.0) |
56.6 (28.8, 80.0) |
0.89 (0.71, 0.95) |
0.65 (0.30, 1) |
| Order | 37 | 71 | 37 | 100.0 | 52.1 |
20 (9, 27) |
100.0 (81.8, 100.0) |
52.6 (23.1, 71.1) |
0.90 (0.74, 0.96) |
0.62 (0.13, 0.89) |
| Family | 73 | 161 | 68 | 93.2 | 42.2 |
34 (12, 44) |
94.1 (80.0, 100.0) |
49.3 (17.6, 62.9) |
0.76 (0.63, 0.88) |
0.65 (0.03, 0.88) |
| Genus | 229 | 613 | 179 | 78.2 | 29.2 |
70 (17, 97) |
95.4 (88.6, 100.0) |
39.5 (9.4, 54.5) |
0.65 (0.45, 0.76) |
0.50 (0.11, 0.70) |
| Species | 609 | 938 | 355 | 58.3 | 37.8 |
114 (15, 175) |
18.7 (2.5, 28.7) |
12.2 (1.6, 18.7) |
0.58 (0.38, 0.72) |
0.47 (0.07, 0.62) |