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Table 2 Results from numerical coverage analysis performed by comparing primer and probe sequences from BactQuant and the published qPCR assays against >670,000 16 S rRNA gene sequences from RDP

From: BactQuant: An enhanced broad-coverage bacterial quantitative real-time PCR assay

  BactQuant Published qPCR Assay Coverage Improvement
A. Perfect match using full length primers and probe
Phyla 91.2%
(31/34)
61.8%
(21/34)
+ 29.4%
Genus 96.2%
(1778/1849)
80.3%
(1485/1849)
+15.8%
Species* 83.5%
(74725/89537)
66.3%
(59459/89646)
+17.2%
All Sequences* 78.0%
(524118/671595)
60.9%
(409584/672060)
+17.1%
B. Perfect match using 8-nt primers with full length probe
Phyla 91.2%
(31/34)
67.7%
(23/34)
+23.5%
Genus 97.7%
(1806/1849)
82.1%
(1518/1849)
+15.6%
Species* 89.1%
(79759/89537)
70.9%
(63533/89646)
+18.2%
All Sequences* 84.4%
(566685/671595)
65.6%
(441017/672060)
+18.8%
  1. The in silico analysis was performed using two sequence matching conditions.
  2. *The difference in number of sequences eligible for in silico evaluation is due to the difference in primer lengths and locations of the two assays.