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Table 3 REL analysis results for three datasets

From: Differential stepwise evolution of SARS coronavirus functional proteins in different host species

Groupsa No. of sequencesd Mean d N -d S e Positively selected site(s)
Spike    
   BAT 4 -0.957  
   PC03 3 -0.904  
   HPEM 14 0.061 49, 75, 77, 144, 239, 244, 311, 344, 778, 860, 861, 1001, 1148, 1163, 1179, 1247
   HPL 11 -0.138  
   PCHP04 27 0.938  
   SARSb 40 0.361 75, 147, 227, 239, 243, 244, 311, 462, 479, 609, 613, 743, 765, 778, 1080, 1163
Replicase    
   BAT 4 -0.985  
   HP03 21 0.008 654
   PCHP04 8 -0.774  
   SARS 31 -0.561  
3'-end ORFs    
   BAT 4 -0.91  
   HPEM 5 -0.42  
   HPML 33 0.152  
   PCHP04 12 -0.571  
   SARSc 40 -0.301  
  1. a. At least 3 sequences are needed for REL analysis, so PC03 groups of dataset 2 and 3 were not analyzed.
  2. b. The upper limit in number of sequences for REL test is 40, so 15 sequences were removed from original SARS group (removed sequences' number: 33, 40, 43, 50, 86, 108, 110, 111, 123, 135, 139, 144, 147, 152, 156)
  3. c. 12 sequences were removed from original SARS group (removed sequences' number: 5, 19, 50, 56, 57, 81, 82, 88, 91, 103, 107, 111)
  4. d. As a rule of thumb, at least 10 sequences are needed to detect selection at a signal site with reliability. So some of the results may be not reliable because of not enough sequences are available for some groups.
  5. e. Because d S could be 0 for some sites, Datamonkey reports d N -d S in place of d N /d S