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Table 2 Detailed results of samples with a single serotype for serotype assignment

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

Sample ID Serotype Total reads mapped against serotype sequences % reads mapped against correct serotype % reads mapped against the second match Serotype(s) identified
      Criterion 1* Criterion 2** Criterion 3***
1 1 4,711 91.9 3.0 1 1 1
2 2 2,245 76.8 8.9 2 2 2
3 3 160 0 75.0 Wrong allocation of serotype Insufficient reads Insufficient reads
4 4 4,985 77.2 10.3 4 4 4
5 5 915 96.1 1.3 5 5 5
6 6B 2,213 96.8 1.0 6 6 6
7 6A 1,241 91.8 3.9 6 6 6
8 7F 222 81.5 6.3 7A/F 7A/F Insufficient reads
9 8 2,955 77.4 3.985 8 8 8
10 9V 4,823 75.5 14.1 9A/V 9A/V 9A/V
11 9N 4,987 88.7 3.0 9N/L 9N/L 9N/L
12 10A 4,257 81.4 6.9 10A/B 10A/B 10A/B
13 11D 1,703 84.9 5.9 11A/D 11A/D 11A/D
14 12F 5,625 94.7 1.9 12/44/46 12/44/46 12/44/46
15 14 2,110 88.3 3.1 14 14 14
16 15B 998 84.9 3.1 15B/C 15B/C 15B/C
17 17F 1,357 72.7 7.3 17F 17F 17F
18 18C 2,418 84.5 3.9 18 18 18
19 19A 3,124 82.0 7.7 19F 19F 19F
20 19F 2,864 87.7 4.9 19A 19A 19A
21 20 169 36.7 27.2 Serotypes 20 and incorrect identification of serotype 23F Insufficient reads Insufficient reads
22 22F 1,948 92.8 3.7 22F/A 22F/A 22F/A
23 23F 1,877 95.1 2.6 23F 23F 23F
24 33F 625 94.4 2.4 33F/A/37 33F/A/37 33F/A/37
  1. * Criterion 1: Any serotype with >15% sequence reads mapped assigned to the sample.
  2. **Criterion 2: Samples with >200 reads considered for further typing AND fulfilled criterion 1.
  3. ***Criterion 3: Samples with >500 reads considered for further typing AND fulfilled criterion 1.
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