Skip to main content

Table 2 Designed primer pair success statistics by cumulative isolate success rate

From: Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

  Forward average success rate Reverse average success rate Total average success rate
Virus Type >25% >50% >75% >85% >90% >25% >50% >75% >85% >90% >25% >50% >75% >85% >90%
HPIV-1 0.99 0.99 0.99 0.99 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.99 0.99
HPIV-3 0.99 0.99 0.98 0.98 0.98 0.99 0.99 0.97 0.97 0.97 0.99 0.99 0.98 0.97 0.97
MeV 0.99 0.97 0.95 0.88 0.88 1.00 0.99 0.97 0.90 0.90 1.00 1.00 0.95 0.89 0.87
MuV 1.00 0.98 0.90 0.88 0.60 1.00 0.97 0.89 0.85 0.54 1.00 0.97 0.89 0.85 0.63
HRSV-A 1.00 0.98 0.94 0.86 0.74 0.98 0.98 0.94 0.86 0.74 1.00 0.98 0.94 0.90 0.76
HRSV-B 1.00 1.00 0.97 0.83 0.76 1.00 1.00 0.97 0.84 0.79 1.00 1.00 0.98 0.91 0.76
HMPV-A 1.00 0.95 0.95 0.93 0.83 0.98 0.93 0.93 0.90 0.81 1.00 0.95 0.93 0.88 0.81
HMPV-B 0.94 0.94 0.94 0.83 0.83 0.97 0.94 0.94 0.83 0.83 0.94 0.94 0.94 0.83 0.80
AVERAGE 0.99 0.98 0.95 0.90 0.83 0.99 0.97 0.95 0.90 0.82 0.99 0.98 0.95 0.90 0.82
MEDIAN 0.99 0.98 0.95 0.88 0.83 0.99 0.98 0.95 0.88 0.82 1.00 0.98 0.94 0.90 0.80
RUBV-G1 * 0.94 0.85 0.73 0.49 0.27 0.90 0.84 0.71 0.51 0.17 0.94 0.85 0.70 0.46 0.26
RUBV-G2 * 0.95 0.90 0.82 0.55 0.55 0.93 0.86 0.75 0.52 0.52 0.95 0.90 0.75 0.55 0.55
AVERAGE (high GC) 0.94 0.88 0.77 0.52 0.41 0.92 0.85 0.73 0.52 0.35 0.94 0.88 0.73 0.51 0.40
MEDIAN (high GC) 0.94 0.88 0.77 0.52 0.41 0.92 0.85 0.73 0.52 0.35 0.94 0.88 0.73 0.51 0.40
  1. * These viruses have a GC content exceeding 67%.