Table 4 Detailed results of samples containing multiple bacterial isolates for pneumococcal identifications and/or serotype assignment
Sample ID | Sample composition (ratio of serotypes) | Total mapped reads per sample | Total reads mapped against serotype sequences | % reads mapped against serotype 19F* | % reads mapped against serotype 3* | % reads mapped against other serotype* | Number of reads mapped against lytA sequences | % reads mapped for S. pneumoniae(typical lytA) | % reads mapped for other viridans streptococci (atypical lytA) |
|---|---|---|---|---|---|---|---|---|---|
(a) Samples with two serotypes tested with PCR 1 | |||||||||
49 | 1:1, 3:19F | 16,318 | 16,318 | 77.8 | 22.1 | 0 | NA | NA | NA |
50 | 1:10, 19F:3 | 17,473 | 17,473 | 80.8 | 18.9 | 0.1 | NA | NA | NA |
51 | 1:10, 3:19F | 19,239 | 19,239 | 85.0 | 14.8 | 0 | NA | NA | NA |
52 | 1:50, 19F:3 | 11,986 | 11,986 | 80.2 | 19.6 | 0 | NA | NA | NA |
53 | 1:50, 3:19F | 4,853 | 4,853 | 82.3 | 17.5 | 0.1 | NA | NA | NA |
54 | 1:100, 19F:3 | 7,447 | 7,447 | 77.4 | 22.2 | 0.1 | NA | NA | NA |
55 | 1:100, 3:19F | 4,251 | 4,251 | 85.5 | 13.7 | 0.2 | NA | NA | NA |
(b) Samples with two serotypes tested with PCR 2 | |||||||||
56 | 1:1, 3:19F | 9,700 | 6,631 | 76.2 | 22.8 | 1.0 | 3,069 | 99.7 | 0.3 |
57 | 1:10, 19F:3 | 17,282 | 12,952 | 79.8 | 19.9 | 0.2 | 4,330 | 99.7 | 0.3 |
58 | 1:10, 3:19F | 10,644 | 7,690 | 84.1 | 15.8 | 0.2 | 2,954 | 99.7 | 0.3 |
59 | 1:50, 19F:3 | 11,623 | 8,666 | 79.2 | 20.7 | 0.2 | 2,957 | 99.6 | 0.4 |
60 | 1:50, 3:19F | 6,378 | 4,392 | 85.2 | 14.6 | 0.3 | 1,986 | 99.4 | 0.6 |
61 | 1:100, 19F:3 | 8,673 | 6,385 | 79.9 | 19.8 | 0.3 | 2,288 | 99.4 | 0.6 |
62 | 1:100, 3:19F | 5,740 | 4,023 | 85.8 | 13.9 | 0.4 | 1,717 | 99.0 | 1.0 |
(c) Samples with proportionately mixed Streptococcus pneumoniae and NCTC 11189 Streptococcus sp. viridans type. tested with PCR 2 | |||||||||
63 | 1:1, NCTC 11189:19F | 10,408 | 7,621 | 99.9 | NA | 0 | 2,787 | 46.6 | 53.4 |
64 | 1:10, 19F:NCTC 11189 | 3,459 | 2,112 | 99.9 | NA | 0.1 | 1,347 | 32.5 | 67.5 |
65 | 1:10, NCTC11189:19F | 1,252 | 842 | 97.7 | NA | 1.8 | 410 | 86.1 | 13.9 |
66 | 1:50, 19F:NCTC 11189 | 18,079 | 10,467 | 100 | NA | 0 | 7,612 | 10.2 | 89.8 |
67 | 1:50, NCTC 11189:19F | 16,336 | 10,172 | 99.8 | NA | 0 | 6,164 | 81.4 | 18.6 |
68 | 1:100,19F:NCTC 11189 | 18,259 | 8,612 | 100 | NA | 0 | 9,647 | 7.6 | 92.4 |
69 | 1:100, NCTC 11189:19F | 8,694 | 3,559 | 100 | NA | 0 | 5,135 | 64.4 | 35.6 |