Table 2. Overview of read and contig sequences.
| Assembly data on filtered reads (%) | ||||||||||||||||||||||
| Number of reads remaining after filtering (%) | Velvet assembly | Clc assembly | ||||||||||||||||||||
| Host reads removal | Contigs | Unassembled reads | Contigs | Unassembled reads | ||||||||||||||||||
| Sample | Quantity of amplified dbDNA used (µg) | Total number of reads | Quality trimming | Duplicate removal | Mapping | Blast W40 | Number | Mean length (nt) | Number. of viral contigs | Number | Mean length (nt) | Number of viral reads | Number of contigs | Mean length (nt) | Number of viral contigs | Number | Mean length (nt) | |||||
| b1 | 5 | 12,899,799 | 12,645,028 (98) | 7,023,394 (54.4) | 6,038,080 (46.8) | 4,204,267 (32.6) | 6,751 | 306 | 11 (0.2) | 3,552,001 (27.5) | 79 | 2,199 (0.02) | 36,190 | 382 | 555 (1.5) | 1,889,481 (14.6) | 86 | |||||
| b2 | 5 | 22,219,022 | 21,950,265 (98.8) | 10,115,989 (45.5) | 8,039,808 (36.2) | 7,879,238 (35.5) | 4,951 | 330 | 11 (0.2) | 3,831,327 (17.2) | 80 | 1,945 (0.01) | 36,539 | 352 | 784 (2.1) | 2,055,437 (9.2) | 87 | |||||
| b3 | 2.5 | 30,302,694 | 29,851,514 (98.5) | 9,238,554 (30.5) | 7,389,992 (24.4) | 3,169,933 (10.5) | 5,324 | 340 | 26 (0.5) | 2,687,511 (8.9) | 70 | 3,435 (0.02) | 10,965 | 555 | 84 (0.8) | 1,210,940 (4) | 72 | |||||
| b4 | 2.5 | 20,235,147 | 19,940,937 (98.5) | 10,952,524 (54.1) | 10,070,367 (49.8) | 7,548,853 (37.3) | 6,532 | 370 | 9 (0.1) | 6,450,250 (31.9) | 79 | 4,657 (0.02) | 30,450 | 374 | 342 (1.1) | 4,081,845 (20.2) | 81 | |||||
| b5 | 2.5 | 10,421,980 | 10,248,486 (98.3) | 4,265,414 (40.9) | 3,669,459 (35.2) | 2,340,303 (22.4) | 1,376 | 235 | 0 | 2,050,634 (19.7) | 76 | 645 (0.01) | 6,001 | 314 | 79 (1.3) | 1,443,245 (13.8) | 81 | |||||
| b6 | 5 | 23,479,591 | 22,961,278 (97.8) | 22,961,130 (97.8) | 18,329,510 (78.1) | 1,057,387 (42.8) | 227 | 275 | 21 (9.2) | 1,920,758 (8.2) | 7 | 15,569 (0.07) | 15,768 | 490 | 202 (1.3) | 5,345,900 (22.8) | 69 | |||||
| b7 | 5 | 15,298,971 | 14,929,686 (97.6) | 14,929,647 (97.6) | 12,630,582 (82.5) | 10,490,399 (68.6) | 3,575 | 216 | 6 (0.2) | 8,320,883 (54.4) | 66 | 12,382 (0.08) | 15,214 | 403 | 216 (1.4) | 6,664,323 (43.6) | 68 | |||||
| b8 | 5 | 22,141,787 | 21,652,636 (97.8) | 21,652,569 (97.8) | 17,122,319 (77.3) | 9,442,165 (42.6) | 1,693 | 368 | 38 (2.2) | 8,314,006 (37.5) | 66 | 170,833 (0.8) | 14,807 | 496 | 184 (1.2) | 5,205,772 (23.5) | 67 | |||||
| b9 | 5 | 19,876,848 | 19,437,257 (97.8) | 19,437,195 (97.8) | 15,342,225 (77.2) | 10,842,780 (54.5) | 25 | 341 | 1 (4) | 10,384,671 (52.2) | 67 | 43,742 (0.2) | 13,586 | 576 | 106 (0.8) | 5,922,754 (29.8) | 68 | |||||
| Mean | - | 19,652,871 | 19,290,787 (98.2) | 13,397,380 (68.2) | 10,959,149 (55.8) | 7,330,592 (37.3) | 3,384 | 309 | 14 (0.4) | 5,279,116 (26.9) | 66 | 28,379 (0.14) | 16,126 | 438 | 284 (1.2) | 3,757,744 (19.1) | 75 | |||||
| Mean deviation | - | 4,519,525 | 4,455,369 | 5,642,449 | 4,352,898 | 2,728,283 | 2,270 | 45 | 10 | 2,745,188 | 13 | 35,071 | 5,832 | 81 | 191 | 1,873,750 | 7 | |||||