Table 1.

Number of samples and mean mappings statistics in each HPV16 and HPV18 diagnostic category.

Diagnostic category	Sequenced samples	Analysed samples		Mean age	Mean numbers in the analysed samples
					Raw reads	Reads mapped to target HPV	Mean coverage	Fraction of genome covered by min. 100×
HPV16
Normala	24	2e	21	49 (32–68)	1.4 M	1.1 M	13516	0.78
ASC-US/LSILb	31	19e		33 (19–54)
CIN2c	47		27	31 (17–61)	0.6 M	0.4 M	4711	0.69
CIN3/AISc	50		27	34 (22–54)	1.0 M	0.8 M	9616	0.76
Cancerc,d	5		5	30 (25–39)	2.4 M	1.7 M	20850	0.67
Total	157		80
HPV18
Normala	3	1e	12	49 (47–52)	38.8 M	23.4 M	292143	0.86
ASC-US/LSILb	13	11e		33 (20–49)
CIN2c	13		9	34 (20–44)	77.1 M	36.5 M	431649	0.86
CIN3/AISc	46		30	34 (24–54)	25.5 M	12.2 M	147747	0.82
Cancer	0		–	–
Total	75		51

^aBy cytology.

^bBy cytology; no cell abnormalities within 4-year follow-up.

^cCytology taken at the time of conisation, with the histological diagnosis presented.

^dIncludes cases of SCC (n = 4) and adenocarcinoma (n = 1).

^eNon-progressive category, samples combined for analysis.