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Table 1 Assessment of CARD and VFDB hits reported by MAIRA

From: MAIRA- real-time taxonomic and functional analysis of long reads on a laptop

Organism Classif. TP (CDS) FN (CDS) TP (Term) FP (Term) FN (Term)
Acinetobacter baumannii CARD 25 3 145 6 65
  VFDB 31 9 31 0 10
Enterococcus faecalis CARD 22 5 24 2 26
  VFDB 23 3 23 0 5
Escherichia coli CARD 69 6 81 22 22
  VFDB 102 27 123 0 36
Klebsiella pneumoniae CARD 63 7 85 20 282*
  VFDB 33 8 34 0 8
Neisseria meningitidis CARD 15 1 16 1 5
  VFDB 31 8 30 0 12
Pseudomonas aeruginosa CARD 55 15 87 7 38
  VFDB 119 16 119 0 22
Staphylococcus aureus CARD 27 2 32 2 7
  VFDB 57 5 55 0 5
Streptococcus agalactiae CARD 4 7 4 4 20
  VFDB 31 0 32 0 1
Streptococcus pneumoniae CARD 17 1 19 8 14
  VFDB 11 2 11 0 4
Streptococcus pyogenes CARD 4 8 4 4 16
  VFDB 29 1 29 0 3
  1. For all ten bacterial species present in a simulated pathogen mock community, we report the number of true postives (TP), false positives (FP) and false negatives (FN), based on the coding sequences (CDS) in the source genomes, and based on the terms reported (Term). () The large false negative value for CARD terms reported for Klebsiella pneumoniae is based on a single CDS that is annotated with over 250 different CARD terms (WP_004176269.1) and thus gives an exaggerated impression