Coverage evaluation of universal bacterial primers using the metagenomic datasets

BMC Microbiology

Table 1 Influence of a single mismatch near the 3′ end in the RDP dataset

Primer	Phylum	Non-coverage rate 4+ (%)	Non-coverage rate 4- (%)
338 F	Lentisphaerae	3.0	100.0
	OP3	5.9	100.0
	Chlamydiae	33.5	99.6
	OD1	36.3	97.8
	Planctomycetes	71.9	98.9
519 F	Nitrospirae	3.0	68.1
	Spirochaetes	1.2	63.3
	Chloroflexi	1.5	59.2
	Planctomycetes	3.4	59.1
	Thermotogae	0.0	54.6
	WS3	2.4	43.4
	OP10	0.0	29.8
	OP8	0.7	21.7
	Cyanobacteria	0.6	21.3
	Gemmatimonadetes	0.6	20.7
	Unclassified Bacteria	2.4	28.4

At the phylum level, non-coverage rates that changed more than 20% under two criteria are listed. “Non-coverage rate 4+” denotes the non-coverage rate when a single mismatch in the last 4 nucleotides was allowed. “Non-coverage rate 4-” denotes the non-coverage rate when mismatches in the last 4 nucleotides were not allowed.

ISSN: 1471-2180