Fig. 2

Visualization methods of WhatsGNU. a Box showing some potential WhatsGNU uses and options. b A histogram of GNU scores of a clinical-CC8-USA300 S. aureus genome “SSTI_179_1”. c Percentage of genomes of clonal complexes (CC) 5, 8, 22, 398,30, and 1 with an exact match for three proteins, SbnD (staphyloferrin B export MFS transporter), TraG (Transfer complex protein), and ArcB (ornithine carbamoyltransferase) from the same genome used in b. d A heatmap of GNU score for key components of the TCA cycle, the glycolytic pathway, and terminal components of the electron transport chain in eighteen different clinical S. aureus isolates. Proteins are listed on the left and isolates numbers on the bottom. In the case of annotated cells, ‘r’ refers to ortholog variant rarity index (OVRI) scores that are less than 0.045. This can be interpreted as an indication that GNU scores this low or lower are very rare in this ortholog group. e Volcano plot showing proteins with a lower average GNU score in a case group (atopic dermatitis) compared to a control group (soft and skin tissue infection). Proteins with lower average GNU score in the AD case group of 18 CC8 S. aureus isolates are shown in red. Proteins with lower average GNU score in the SSTI control group of 49 CC8 S. aureus isolates are shown in green. The P value is from a Mann–Whitney–Wilcoxon test. A second volcano plot with Y-axis as OVRI is shown in supplementary figure 3. Example WhatsGNU reports are in the supplementary data