This PDF file includes:

• fig. S1. Bioinformatics strategy for rRNA copy number estimation and variant discovery.
  
• fig. S2. rDNA copy number estimation in human and mouse.
  
• fig. S3. Tertiary structure of rRNA variants.
  
• fig. S4. Properties of detected rDNA variants detected in rRNA genes in human.
  
• fig. S5. The number of variants stratified by each population.
  
• fig. S6. rRNA variants with correlated AF in human.
  
• fig. S7. rRNA variants that are differentially expressed between mouse tissues that localize to known functional centers of the ribosome.
  
• fig. S8. Genomic AF and polysome expression.
  
• Legends for tables S1 to S5
  
• table S6. Summary of rRNA variants detected in mouse strains from the Mouse Genomes Project.
  
• Legends for tables S7 and S8

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Other Supplementary Material for this manuscript includes the following:

• table S1 (Microsoft Excel format). Population stratification of rDNA copy number (V_st > 0.2).
  
• table S2 (Microsoft Excel format). Detected rRNA indel variants.
  
• table S3 (Microsoft Excel format). Detected rDNA variants in human that occur at positions of rRNA known to be modified in eukaryotes.
  
• table S4 (Microsoft Excel format). Human individuals with variants in intersubunit bridges.
  
• table S5 (Microsoft Excel format). rRNA variants whose AFs are stratified by populations.
  
• table S7 (Microsoft Excel format). Common rRNA variant positions in mouse and human.
  
• table S8 (Microsoft Excel format). Log intensity of proteins detected from quantitative mass spectrometry analysis.