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

Table 2 Mapping of Illumina reads generated for specimen HH015 to HPV reference genome sequences

HPV type	Genbank accession of reference sequence	Individual mapping			Simultaneous mapping
HPV type	Genbank accession of reference sequence	Read count^€	Coverage^#	Percentage of genome sequenced	Read count^€	Coverage^#	Percentage of genome sequenced
39^*	M62849	1452838	7604.5	100.0	1450445	7592.9	100.0
40^*	X74478	267072	1384.5	100.0	267072	1384.5	100.0
16^*	FJ610149	204214	1059.0	100.0	204212	1059.0	100.0
70^*	HPU21941	32187	171.0	97.6	3295	17.1	97.6
74	AF436130	27099	142.7	98.7	26802	139.3	98.7
56	EF177179	18510	97.4	100.0	18409	96.9	100.0
30	X74474	8781	45.9	99.9	8612	45.0	99.9
45^*	EF202160	2873	15.9	94.7	774	4.0	94.4
71^*	NC002644	2106	10.8	99.6	2088	10.7	99.6
55^*	HPU31791	1400	14.2	51.8	587	3.1	49.2
59^*	X77858	1342	7.6	91.2	692	3.6	91.2
90	AY057438	1136	5.9	98.0	1116	5.7	98.0
35	PPH35CG	1109	6.5	88.6	720	3.8	88.4
86	AF349909	683	5.3	66.0	680	5.3	66.0
53^*	NC001593	682	4.6	77.9	462	2.4	77.6
81^*	AJ620209	308	2.2	72.5	308	2.2	72.5
84^*	AF293960	28	1.9	7.6	11	0.1	4.7

ISSN: 1743-422X