Skip to main content

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) Pearson’s correlation coefficient between removal of vSNPs and recovery of fSNPs Pearson’s 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 − 0.13
E. faecium 94.38 9 (5; 10) 3 (2; 5) 0.47 − 0.45
K. pneumoniae 84.38 549 (62; 112) 73 (13; 41) 0.76 − 0.44
L. pneumophila 99.06 12 (0; 8) 3 (0; 1) 0.99 − 0.63
L. monocytogenes 98.42 2 (0; 1) 0 (0; 0) 0.49 − 0.43
N. gonorrhoeae 99.17 0 (0; 0) 0 (0; 0) 0.34 − 0.09
P. aeruginosa 97.43 9 (2; 14) 1 (0; 1) 0.50 − 0.11
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 − 0.10
T. pallidum 39.75 45 (34; 52) 6 (5; 4) 0.63 − 0.48
V. cholerae 91.32 9 (5; 16) 2 (1; 3) 0.76 − 0.56