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

Table 3 Detailed results of samples with a single serotype for pneumococcal identification and 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			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
26	2	271	32.5	23.6	ID of serotype 6	ID of serotype 6	Insufficient reads	4,123	0
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
28	4	416	39.2	31.3	ID of serotype 1	ID of serotype 1	Insufficient reads	4,595	0
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
45	20	128	28.9	26.6	ID of serotype 23F	Insufficient reads	Insufficient reads	1,946	0
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

^ Denominator - total number of reads mapped against serotype/group specific sequences.
*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