Table 2. Amplicon Coverage and Model Utilization.
Amplicon sequencing data were evaluated using the 20 taxa HM-782D and 48 taxa 48G-Eq samples. Several of the amplicons where predicted, by in silico PCR, to have poor amplification for the species present in the SILVA 16S rRNA database. A species is ‘Predicted to amplify’ by a primer pair if the primers amplify 80% or more of the 16S rRNA sequences belonging to the species in the database. Predictions of poor amplification were empirically confirmed by the negligible number of species with a significant number of mapped reads (> 1% of total) when these two mock community samples were sequenced.
| Variable Region Amplicon | % SILVA Species Predicted to Amplify | HM-782D (20-taxa consortium) |
48G-Eq (48 taxa consortium; even) |
||
|---|---|---|---|---|---|
| % Total Reads | % Species >1% Total Reads | % Total Reads | % Species >1% Total Reads | ||
| V1 | 0.2% | 5.9% | 0 | 3.3% | 0 |
| V1-V2 | 37.9% | 4.6% | 24 | 2.4% | 21 |
| V2 | 91.3% | 7.6% | 28 | 9.7% | 21 |
| V3_1 | 0.01% | 9.7% | 1 | 0.5% | 2 |
| V3_2 | 98.3% | 10.6% | 31 | 14.6% | 23 |
| V4 | 97.7% | 7.9% | 32 | 7.1% | 23 |
| V5-V6 | 96.6% | 7.1% | 27 | 6.3% | 21 |
| V5_1 | 73.8% | 5.6% | 0 | 1.7% | 0 |
| V5_2 | 0.1% | 5.5% | 1 | 4.6% | 0 |
| V6_1 | 98.6% | 6.4% | 27 | 14.2% | 21 |
| V6_2 | 0.04% | 5.30% | 0 | 7.6% | 0 |
| V6_3 | 0.04% | 5.8% | 0 | 8.3% | 0 |
| V7-V8 | 94.0% | 9.0% | 30 | 9.1% | 22 |
| V9 | 0.1% | 7.1% | 0 | 5.8% | 0 |