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

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

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

* Criterion 1: Any serotype with >15% sequence reads mapped assigned to the sample.
**Criterion 2: Samples with >200 reads considered for further typing AND fulfilled criterion 1.
***Criterion 3: Samples with >500 reads considered for further typing AND fulfilled criterion 1.

ISSN: 1471-2180