Table 2.

Analysis of reads and contigs generated in this study.

	Sample 1			Sample 2			Sample 3
	Method 1	Method 2	Method 3	Method 1	Method 2	Method 3	Method 1	Method 2	Method 3
Number of reads	5,178,341	4,529,496	4,859,283	1,233,706	2,072,054	4,014,133	924,765	4,417,682	3,771,214
Average length of reads (bp)	145.67	241.50	183.32	64.60	183.24	183.02	123.08	236.15	237.07
Number of contigs	1884	3342	6131	1197	26,361	128,514	13,994	111,203	107,111
Total length of contigs (bp)	262,278	886,853	1,748,273	562,811	10,016,341	64,285,331	2,218,132	38,388,478	51,957,239
Average length of contigs (bp)	139.21	265.37	285.15	470.18	379.97	500.22	158.51	345.21	485.08
Number of contigs mapped to viruses including phages	51	234	136	131	851	2503	1589	6467	10,538
The percentage of contigs mapped to viruses including phages	2.71%	7.00%	2.22%	10.94%	3.23%	1.95%	11.35%	5.82%	9.84%
Number of contigs mapped to viruses excluding phages	48	228	126	106	457	280	644	1676	1212
The percentage of contigs mapped to viruses excluding phages	2.55%	6.82%	2.06%	8.86%	1.73%	0.22%	4.60%	1.51%	1.13%
Number of bacteria contigs	1041	1503	3910	192	3204	12,627	907	6423	7387
Number of archaea contigs	0	8	0	9	19	68	0	10	9
Number of eukaryote contigs	68	90	340	67	933	1700	1338	6533	1597
Number of unassigned contigs	40	58	92	30	332	902	194	731	940
Number of no-hit contigs	75	1080	984	690	20,576	108,003	9093	85,288	80,684
Number of classified viral families identified excluding phages	2	3	4	8	16	13	13	17	14
Number of classified viral genera identified excluding phages	2	3	4	8	23	19	18	23	19
Accession number (SRR)	5078294	5078297	5078298	5078299	5078300	5078301	5078288	4051861	4051862