Table 1 Percentage of correct identification of pneumococcal serogroup/serotypes based on different cut-off limits on number of reads
Sample category | Definition for interpretation cut-off* | Median no. reads mapped against serotype/group (IQR) | Mean percentage of reads aligned against correct serotype (95% CI) | Mean percentage of reads aligned against second serotype (if present) (95% CI) | No. of samples | Percentage of correct ID |
|---|---|---|---|---|---|---|
PCR1 (serotype assignment only) | All samples** | 2,162 (1,059–3,691) | 80.5% (72.0–89.0%) | 8.8% (2.7–14.9%) | 24 | 91.7% |
Samples with >200 reads mapped against serotypes | 2,229 (1,328–4,257) | 86.2% (83.1–89.3%) | 5.0% (3.7–6.34%) | 23 | 100% | |
Samples with >500 reads mapped against serotypes | 2,245 (1,530–4,371) | 86.5% (83.3–89.7%) | 4.9% (3.5–6.3%) | 21 | 100% | |
PCR2 (serotype and ID) | All samples** | 1,658 (807–2,573) | 80.7% (72.9–88.5%) | 7.5% (4.3–10.7%) | 24 | 87.5% |
Samples with >200 reads mapped against serotypes | 1,683 (898–2,574) | 83.0% (76.4–89.6%) | 6.6% (3.8–9.4%) | 23 | 91.3% | |
Samples with >500 reads mapped against serotypes | 1,951 (1,178–2,633) | 87.1% (85.1–89.1%) | 4.8% (2.3–7.3%) | 19 | 100% |