Table 1. Description of samples positive for chikungunya and dengue virus by real-time reverse transcription-PCR with corresponding Illumina mapping data, United Kingdom, 2017^a (n = 26 samples).

Sample	Ct value	Estimated genome copy number in the sample (/mL)	Sample type	Total reads (R1 + R2)b	% reads mapping to reference viral genome	% 20x coverage	% 10x coverage	Reference virusc	Reference size (nts)
CHIKV 1	14.72	2.12E + 10	Plasma	1,113,560	78.32	99.59	99.72	CHIKV	11,826
CHIKV 2	20.06	5.49E + 08	Serum	1,278,624	98.48	99.14	99.47	CHIKV	11,826
CHIKV 3	21.41	2.18E + 08	Plasma	1,391,258	95.23	98.86	99.37	CHIKV	11,826
CHIKV 4	22.74	8.76E + 07	Plasma	888,968	19.16	97.08	97.32	CHIKV	11,826
CHIKV 5	23.77	4.33E + 07	Plasma	1,357,606	97.13	99.16	99.58	CHIKV	11,826
CHIKV 6	25.4	1.42E + 07	Serum	3,236,848	34.88	97.80	98.40	CHIKV	11,826
CHIKV 7	25.76	1.11E + 07	Plasma	3,748,070	72.77	99.04	99.56	CHIKV	11,826
CHIKV 8	28.17	2.13E + 06	Plasma	1,499,952	28.41	98.69	99.00	CHIKV	11,826
CHIKV 9	30.08	5.76E + 05	Serum	1,035,026	6.66	95.98	98.22	CHIKV	11,826
CHIKV 10	30.37	4.72E + 05	Serum	1,575,222	16.84	97.39	98.01	CHIKV	11,826
CHIKV 11	30.66	3.87E + 05	Serum	1,143,054	13.52	95.36	96.96	CHIKV	11,826
CHIKV 12	30.95	3.17E + 05	Serum	1,507,380	10.93	96.11	96.52	CHIKV	11,826
CHIKV 13	32.2	1.35E + 05	Serum	1,323,920	5.03	88.47	89.38	CHIKV	11,826
CHIKV 14	32.57	1.05E + 05	Serum	1,479,404	21.72	96.32	96.93	CHIKV	11,826
DENV 1	16.29	4.21E + 09	Plasma	439,292	93.44	99.51	99.58	DENV 1	10,735
DENV 2	16.85	2.83E + 09	Serum	513,472	92.56	99.40	99.58	DENV 1	10,735
DENV 3	17.67	1.58E + 09	Plasma	738,814	92.53	99.58	99.58	DENV 2	10,723
DENV 4	18.20	1.09E + 09	Serum	477,368	93.97	98.73	99.12	DENV 2	10,723
DENV 5	19.73	3.67E + 08	Serum	915554	89.65	99.14	99.40	DENV 2	10,723
DENV 6	21.22	3.61E + 07	Serum	3,587,926	83.87	99.68	99.69	DENV 4	10,649
DENV 7	23.76	2.11E + 07	Serum	4,146,678	2.17	86.99	89.13	DENV 1	10,735
DENV 8	24.8	1.01E + 07	Serum	777,264	69.23	99.56	99.58	DENV 3	10,707
DENV 9	25.28	7.17E + 06	Plasma	787,728	26.97	98.77	98.81	DENV 2	10,723
DENV 10	26.98	2.15E + 06	Serum	596,240	6.58	93.47	93.97	DENV 3	10,707
DENV 11	28.69	6.39E + 05	Serum	1,034,698	3.73	94.44	94.70	DENV 1	10,735
DENV 12	31.29	1.01E + 05	Serum	1,374,766	0.47	71.46	77.76	DENV 1	10,735

CHIKV: chikungunya virus; Ct: cycle threshold; DENV: dengue virus.

^a The Illumina mapping data presented in the table were obtained in 2017 on samples that had been collected and found positive for chikungunya or dengue virus by real-time reverse transcription-PCR in 2016.

^b ‘R1 + R2’ indicates paired-end sequencing.

^c For DENV the serotype is also indicated.