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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

StudyMean 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 fSNPsPearson’s correlation coefficient between removal of vSNPs and percentage of target organism
A. baumannii97.3089 (43; 165)57 (10; 113)0.990.25
C. difficile76.74299 (397; 379)27 (16; 32)0.450.23
E. faecalis89.9630 (19; 33)4 (3; 5)0.65− 0.13
E. faecium94.389 (5; 10)3 (2; 5)0.47− 0.45
K. pneumoniae84.38549 (62; 112)73 (13; 41)0.76− 0.44
L. pneumophila99.0612 (0; 8)3 (0; 1)0.99− 0.63
L. monocytogenes98.422 (0; 1)0 (0; 0)0.49− 0.43
N. gonorrhoeae99.170 (0; 0)0 (0; 0)0.34− 0.09
P. aeruginosa97.439 (2; 14)1 (0; 1)0.50− 0.11
S. enterica95.0197 (91; 87)7 (6; 12)0.140.02
S. aureus91.4250 (22; 50)9 (3; 9)0.54− 0.10
T. pallidum39.7545 (34; 52)6 (5; 4)0.63− 0.48
V. cholerae91.329 (5; 16)2 (1; 3)0.76− 0.56