TABLE 3.
Coverage evaluation of primers based on the amoA gene sequencesa
| Primer | Clade (% [no./total]) |
AOB (% [no./total]) | |||
|---|---|---|---|---|---|
| A.1 | A.2 | A | B | ||
| A189Y | 99 (282/286) | 97 (672/690) | 98 (954/976) | 94 (50/53) | 98 (1,944/1,977) |
| HD616N | 97 (267/274) | 96 (76/79) | 97 (343/353) | 67 (31/46) | 51 (2,531/4,955) |
| CA209f | 98 (278/285) | 86 (506/586) | 90 (784/871) | 98 (63/64) | 98 (2,429/2,506) |
| C576r | 98 (277/283) | 87 (72/83) | 95 (349/366) | 91 (30/33) | 0 (0/5,051) |
| A378f | 78 (188/241) | 73 (66/91) | 77 (254/332) | 0 (0/36) | 0 (0/4,298) |
| C616r | 84 (231/274) | 58 (46/79) | 78 (277/353) | 2 (1/46) | 0 (0/4,951) |
| A189 | 76 (217/286) | 60 (415/690) | 65 (632/976) | 85 (45/53) | 53 (1,045/1,977) |
| A682 | 67 (130/194) | 26 (24/92) | 54 (154/286) | 73 (35/48) | 66 (412/626) |
a
Extracted from metagenomic or metatranscriptomic data sets in public databases, as described in Table S1. A sequence was considered to be covered by this primer if it had no mismatches or only one mismatch that was not located in the last four positions near the 3′ end. The numbers in parentheses denote the number of sequences matched with each primer and the number of extracted sequences that cover the region of this primer.