Next-generation sequencing of cervical DNA detects human papillomavirus types not detected by commercial kits

Table 3 Mapping of Illumina reads generated for specimen HH015 to HPV long control region (LCR) sequences

HPV type	Genbank accession of reference sequence	Individual mapping				Simultaneous mapping
HPV type	Genbank accession of reference sequence	Read count^€	Coverage^#	Percentage of LCR sequenced	Identity°	Read count^€	Coverage^#	Percentage of LCR sequenced	Identity°
39^*	M62849	131419	6916.8	100	100	131417	6916.7	100	100
16^*	FJ610149	20258	998.3	100	99.8	20258	998.3	100	99.8
40^*	X74478	19984	1147.5	100	99.6	19984	1147.5	100	99.6
56	EF177179	1940	100.2	100	99.6	1940	100.2	100	99.6
74	AF436130	1565	91.9	88.6	97.9	1560	91.6	88.6	97.9
30	X74474	789	40.9	99.2	99.2	789	40.9	99.2	99.2
71^*	NC002644	176	10.0	92.9	100	176	10.0	92.9	100
70^*	HPU21941	97	4.7	93.6	99.9	95	4.6	93.6	99.9
35	PPH35CG	79	4.4	84.8	99.6	79	4.4	84.8	99.6
45^*	EF202160	68	3.7	92.5	98.9	68	3.7	92.5	98.9
59^*	X77858	57	3.4	83.6	100	57	3.4	83.6	100
90	AY057438	55	3.6	87.4	98.6	55	3.6	87.4	98.6
55^*	HPU31791	54	5.7	53.3	98.7	18	2.0	50.0	98.7
86	AF349909	50	4.6	55.0	98.0	50	4.6	55.0	98.0
81^*	AJ620209	29	2.4	61.8	100	29	2.4	61.8	100
53^*	NC001593	24	2.7	45.7	98.6	24	2.7	45.7	98.6

^* HPV types detected by the Roche Linear Array HPV Genotyping kit.
^€ Number of reads mapped to the reference sequence using CLC Genomics Workbench 4.6.1 (limit 3, cost 2, global alignment).
^# Average number of times each base was sequenced.
° Percentage identity of the assembled contig to the reference sequence.

ISSN: 1743-422X