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Table 1 Simulation parameter values and mean of inferred parameter values across 5 simulation and inference replicates

From: TreeToReads - a pipeline for simulating raw reads from phylogenies

   Case Study 1 – Salmonella enterica Bareilly  
   Input Inferred   
    Close ref Far ref  
Number of SNPs   100 98.6 (1.4) 38,384 (mutations)  
     154 (3) variable sites  
RF distance   - 33 (1) 33 (1)  
Outbreak clade monophyletic   - 5/5 5/5  
Base frequencies A 0.238787 0.24 (0.03) 0.25 (0.0)  
  C 0.261361 0.26 (0.03) 0.25 (0.0)  
  G 0.261132 0.24 (0.03) 0.25 (0.0)  
  T 0.238720 0.27 (0.03) 0.24 (0.0005)  
GTR rate Matrix ac 0.4 0.1 (0.7) 1.5 (0.6)  
  ag T 3.0 91 (160) 5.4 (2.0)  
  at 0.5 21 (39) 1.0 (0.6)  
  cg 0.1 0.1 (0.2) 1.5 (0.7)  
  ct 4.4 66 (112) 5.3 (1.9)  
  gt 1 1.0 (0.0) 1.0 (0.0)  
Coverage   20 17.04 (0) 15.45 (0)  
   Case Study 2 – Listeria monocytogenes  
   Input Inferred   
Number of SNPs   500 494.8 (1.6)   
RF distance   - 0.0 (0)   
Base frequencies A 0.311521 0.30 (0.01)   
  C 0.190709 0.20 (0.01)   
  G 0.189125 0.20 (0.007)   
  T 0.308645 0.29 (0.007)   
GTR rate Matrix ac 1.2070 1.1 (0.1)   
  ag 5.9306 5.3 (0.8)   
  at 1.7425 1.8 (0.2)   
  cg 0.4610 0.3 (0.2)   
  ct 5.1238 5.1 (0.7)   
  gt 1 1.0 (0.0)   
Coverage   40 37.49 (0)   
Difference from INDELible gap distribution   0 0.0 (0)   
  1. Standard deviations of parameter values shown in parentheses