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
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%

The in silico analysis was performed using two sequence matching conditions.

*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.

Liu et al.

Liu et al. BMC Microbiology 2012 12:56   doi:10.1186/1471-2180-12-56

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