Science Advances

The PDF file includes:

• Fig. S1. DFT-simulated distribution of electronic charge density for Si₁C₄ defect.
• Fig. S2. DFT-simulated distribution of electronic charge density for Si₂C₄ defect.
• Fig. S3. DFT-simulated distribution of electronic charge density for Si₂C₅ (type 1) defect.
• Fig. S4. DFT-simulated distribution of electronic charge density for Si₂C₅ (type 2) defect.
• Fig. S5. Strain analysis for S₁C₃ defect.
• Fig. S6. More complex defect structures observed in the STM experiment on STEM sample of graphene.

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Other Supplementary Material for this manuscript includes the following:

• Jupyter notebook (atom-finding accuracy versus noise) (.ipynb format)