Table 2 Effect of applying the taxonomic filter in the variant analysis of samples of the bacterial dataset
From: Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
Study | Mean percentage of target organism (%) | Mean number of vSNPs removed (median; IQR) | Mean number of fSNPs recovered (median; IQR) | Pearsonās correlation coefficient between removal of vSNPs and recovery of fSNPs | Pearsonās correlation coefficient between removal of vSNPs and percentage of target organism |
|---|---|---|---|---|---|
A. baumannii | 97.30 | 89 (43; 165) | 57 (10; 113) | 0.99 | 0.25 |
C. difficile | 76.74 | 299 (397; 379) | 27 (16; 32) | 0.45 | 0.23 |
E. faecalis | 89.96 | 30 (19; 33) | 4 (3; 5) | 0.65 | āā0.13 |
E. faecium | 94.38 | 9 (5; 10) | 3 (2; 5) | 0.47 | āā0.45 |
K. pneumoniae | 84.38 | 549 (62; 112) | 73 (13; 41) | 0.76 | āā0.44 |
L. pneumophila | 99.06 | 12 (0; 8) | 3 (0; 1) | 0.99 | āā0.63 |
L. monocytogenes | 98.42 | 2 (0; 1) | 0 (0; 0) | 0.49 | āā0.43 |
N. gonorrhoeae | 99.17 | 0 (0; 0) | 0 (0; 0) | 0.34 | āā0.09 |
P. aeruginosa | 97.43 | 9 (2; 14) | 1 (0; 1) | 0.50 | āā0.11 |
S. enterica | 95.01 | 97 (91; 87) | 7 (6; 12) | 0.14 | 0.02 |
S. aureus | 91.42 | 50 (22; 50) | 9 (3; 9) | 0.54 | āā0.10 |
T. pallidum | 39.75 | 45 (34; 52) | 6 (5; 4) | 0.63 | āā0.48 |
V. cholerae | 91.32 | 9 (5; 16) | 2 (1; 3) | 0.76 | āā0.56 |