Table 1.

Composition of sequence data and de novo assembly statistics

Sample	Sample ID	Virus	Copies viral RNA used	Versiona	Reads aligning to viral referenceb (%)	rRNAc (%)	Hostd (%)	CDS covered by all contigse (%)	Average coverage in target region	Genes intactf
NL4-3	D615	HIV	10 000	1	67.1	0.3	3.5	100	36 021	9
Clinical sample A	D614	HIV	10 000	1	7.1	32.3	32.5	100	3869	9
Clinical sample A	D613	HIV	1 000	1	6.5	25.9	28.8	96	3489	7
Clinical sample B	D616	HIV	800	1	5.9	18.6	18.9	100	3109	9
Clinical sample C	D617	HIV	200	1	2.2	17.5	12.8	100	965	9
NL4-3	D619	HIV	10 000	2	68.7	0.6	4.6	100	38 725	9
Clinical sample B	D620	HIV	800	2	1.1	16.8	18.2	100	661	9
Clinical sample C	D621	HIV	200	2	0.4	14.8	8.8	97	233	8
Clinical sample B	G15482	HIV	200	2	1.3	18.2	27.9	100	647	9
Clinical sample B	G15480	HIV	100	2	1.7	17.5	28.0	99	385	8
WNV clone	G15493	WNV	10 000	2	31.1	0.11	47.6	100	14 822	10
WNV clone	G15494	WNV	1500	2	14.5	0.09	59.1	100	6925	10
WNV clone	G15495	WNV	1000	2	14.3	0.09	59.1	99	6800	9
WNV clone	G15496	WNV	750	2	13.7	0.08	59.1	100	6594	10
WNV clone	G15497	WNV	500	2	13.9	0.10	59.8	100	6681	10
WNV clone	G15498	WNV	250	2	14.3	0.08	59.0	100	6786	10
WNV clone	G15499	WNV	150	2	15.1	0.09	58.7	100	7253	10
WNV clone	G15500	WNV	100	2	13.8	0.09	59.4	100	6576	10
Clinical sample 1	V6100	RSV	30 470	2	16.6	31.8	37.0	100	5599	10
Clinical sample 2	V6103	RSV	1795	2	10.1	36.7	26.5	100	3386	10

^aNuGEN’s Ovation RNA-Seq version 1 or 2 system. ^bFor HIV, the viral reference genome used was HXB2. For WNV, the viral reference genome used was NY99. For RSV, the viral reference genome used was RSV A2. ^cPercent of reads aligning to both cytoplasmic and mitochondrial rRNA. For HIV and RSV, human rRNA sequences were used. For WNV, hamster rRNA sequences were used. ^dFor HIV and RSV, the host used was human. For WNV, the host used was hamster. ^eThose samples with 100% genome covered were in a single contig except V6103 which was covered in two contigs. Those with less than 100% were covered in two contigs except D613 which was covered in three contigs. ^fFor HIV, the total number of genes is 9. For WNV and RSV, the total number of genes is 10.