Skip to main content

Table 3 Detailed results of samples with a single serotype for pneumococcal identification and 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 No of reads mapped for S. pneumoniae(typical lytA) No of reads mapped for viridans streptococci (atypical lytA)
      Criterion 1* Criterion 2** Criterion 3***   
25 1 776 81.2 7.2 1 1 1 2,073 1
26 2 271 32.5 23.6 2 and incorrect 2 and incorrect Insufficient reads 4,123 0
ID of serotype 6 ID of serotype 6
27 3 1,127 78.9 8.8 3 3 3 4,646 0
28 4 416 39.2 31.3 4 and incorrect 4 and incorrect Insufficient reads 4,595 0
ID of serotype 1 ID of serotype 1
29 5 1,181 92.6 5.0 5 5 5 1,048 0
30 6B 2,501 97.4 1.3 6 6 6 1,294 0
31 6A 898 92.7 3.0 6 6 6 490 0
32 7F 360 89.2 5.0 7A/F 7A/F Insufficient reads 292 0
33 8 1,868 74.4 6.5 8 8 8 7,396 0
34 9V 2,095 83.2 4.5 9A/V 9A/V 9A/V 2,992 0
35 9N 5,238 91.7 2.5 9N/L 9N/L 9N/L 5,934 0
36 10A 4,341 82.0 7.8 10A/B 10A/B 10A/B 14,623 0
37 11D 1,951 85.3 7.0 11A/D 11A/D 11A/D 4,844 0
38 12F 5,224 92.6 1.7 12/44/46 12/44/46 12/44/46 5,881 0
39 14 1,968 88.2 3.6 14 14 14 4,624 0
40 15B 986 89.6 3.8 15B/C 15B/C 15B/C 1,184 0
41 17F 1,178 71.7 7.1 17F 17F 17F 5,387 0
42 18C 2,699 97.0 0.8 18 18 18 4,502 0
43 19A 2,644 82.2 7.7 19F 19F 19F 3,079 0
44 19F 2,598 87.1 5.7 19A 19A 19A 5,570 0
45 20 128 28.9 26.6 20 and incorrect Insufficient reads Insufficient reads 1,946 0
ID of serotype 23F
46 22F 1,683 92.5 4.2 22F/A 22F/A 22F/A 2,107 0
47 23F 1,633 94.2 2.1 23F 23F 23F 1,404 0
48 33F 475 93.5 2.1 33F/A/37 33F/A/37 Insufficient reads 496 0
  1. ^ Denominator - total number of reads mapped against serotype/group specific sequences.
  2. *Criterion 1: Any serotype with >15% sequence reads mapped assigned to the sample.
  3. **Criterion 2: Samples with >200 reads considered for further typing AND fulfilled criterion 1.
  4. ***Criterion 3: Samples with >500 reads considered for further typing AND fulfilled criterion 1.
\