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Table 1 Percentage of correct identification of pneumococcal serogroup/serotypes based on different cut-off limits on number of reads

From: Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

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%
  1. *Criteria for serotype allocation. Each category fulfilled the minimum criterion of >15% reads out of total reads assigned to the sample.
  2. **Criterion of >15% reads out of total reads mapped assigned to the sample.
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