Table 2.
Summary of the number of reads and contigs at each step in the data processing pipeline.
| Sample | Reads Pre-QC | Reads Post-QC | Contigs Post-Assembly (Mean Length; Standard Deviation; Median Length) | Contigs Assigned | Virus Contigs Assigned (Mean Length ± Standard Deviation; Median Length) | Percent of Virus Contigs |
|---|---|---|---|---|---|---|
| 30 July—nearshore | 13,403,832 | 11,608,892 | 480,233 (692; 589; 526) |
212,156 | 349 (681; 326; 563) | 0.16 |
| 30 July—mid-harbour | 13,206,316 | 11,246,470 | 433,927 (823; 1540; 563) |
256,277 | 397 (626; 341; 526) | 0.15 |
| 13 August—nearshore | 12,758,364 | 11,040,814 | 398,774 (741; 1493; 531) |
196,128 | 488 (767; 405; 650) | 0.25 |
| 13 August—mid-harbour | 13,104,992 | 11,414,576 | 416,468 (820; 1060; 571) |
273,693 | 662 (688; 357; 570) | 0.24 |
| 27 August—nearshore | 15,685,750 | 13,953,600 | 374,464 (661; 923; 498) |
128,233 | 484 (693; 300; 592) | 0.38 |
| 27 August—mid-harbour | 16,101,196 | 14,751,904 | 233,868 (833; 1567; 568) |
183,817 | 232 (731; 460; 555) | 0.13 |
| 10 September—nearshore | 16,228,148 | 14,257,158 | 418,490 (609; 848; 487) |
110,567 | 463 (736; 327; 642) | 0.42 |
| 10 September—mid-harbour | 15,411,142 | 13,561,346 | 443,692 (568; 765; 474) |
64,142 | 604 (753; 320; 673) | 0.94 |
| 24 September—nearshore | 14,689,040 | 12,764,018 | 367,778 (629; 873; 491) |
112,144 | 372 (810; 612; 676) | 0.33 |
| 24 September—mid-harbour | 13,151,390 | 11,228,970 | 296,813 (776; 1094; 550) |
185,913 | 104 (870; 1257; 489) | 0.06 |