Fig. 2

Illustration of what P-site and A-site mean and how offset is determined. a The ribosome protected fragment is usually around 30 nt. The positions being translated are P-site (3 nt) and A-site (3 nt). A-site should be used to calculate the translational speed of each codon. The distance from the 5′ end of the RPF to the 5′ of P-site is defined as “P-site offset”. When the position of P-site is determined, A-site is just 3 nt downstream of the P-site. b In the ribosome profiling data, we counted the percentages of RPF reads mapped to the different frames. Frame0 represents the RPF reads with 5′ end mapped to the first codon position. Frame1 means the 5′ end of RPF reads was mapped to the second codon position. Frame2 means the third codon position. c The 5′ end of RPF reads usually peaks at the upstream of start codon ATG. The distance from the peak to the start codon is the P-site offset. d The P-site offset of RPF reads with different lengths