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Table 2 Substitutions between the genomes of PVS isolates H95 and H00

From: Construction and characterization of an infectious cDNA clone of potato virus S developed from selected populations that survived genetic bottlenecks

  ORF1 ORF2 ORF3 ORF4 ORF5 ORF6 Total
Nt (%) Nt (%) Nt (%) Nt (%) Nt (%) Nt (%) Nt (%)
Nucleotide substitutions Ti 260 81.0 22 81.5 12 85.7 4 100 3 100 1 100 302 81.6
Tv 61 19.0 5 18.5 2 14.3 0 0 0 0 0 0 68 18.4
Ti/Tv 4.26 4.40 6.00 4.44
S 232 72.3 18 66.7 13 92.9 3 75 2 66.7 0 0 268 72.4
NS 89 27.7 9 33.3 1 7.1 1 25 1 33.3 1 100 102 27.6
Ka/Ks 0.38 0.50 0.08 0.33 0.50 0.38
Total 321 5.4 27 3.9 14 4.3 4 2.0 3 0.3 1 0.4 370 4.4
  Replicase TGBp1 TGBp2 TGBp3 CP CRP Total
Aa (%) Aa (%) Aa (%) Aa (%) Aa (%) Aa (%) Aa (%)
Amino acids substitutionsa 0–3 22 27.5 2 28.6 0 0 0 0 0 0 1 100 25 27.5
4 22 27.5 0 0 0 0 0 0 1 100 0 0 23 25.3
5 36 45.0 5 71.4 1 100 1 100 0 0 0 0 43 47.3
Total 80 4.1 7 3.1 1 0.9 1 1.5 1 0.3 1 1.1 91 3.3
  1. Percentage in italic letters indicate the proportion of different substitutions shown in the left column to the total substitutions
  2. aSubstitutions were evaluated using the Structure-Genetic (SG) scoring system. The SG values range from 0 (most drastic change) to 5 (most frequent substitution)
  3. Nt Nucleotides, Aa Amino acids, Ti Transition, Tv Transversion, S Synonymous, NS Nonsynonymous,
  4. Ka/Ks: The ratio of nonsynonymous to synonymous substitution rate