Table 1. Distribution of viral reads in 2009 H1N1 influenza samples.
| SAMPLE | TOTAL ALIGNED READS | TOTAL VIRAL READS | FLU | % FLU (TOTAL ALIGNED READS) | % FLU (VIRAL READS) | PHAGE | MLV | OTHER VIRAL |
| Ont-61 | 574,838 | 2,649 | 2,649 | 0.46% | 100% | - | - | - |
| Ont-69 | 25,500 | 2,243 | 2,243 | 8.8% | 100% | - | - | - |
| Ont-84 | 947,111 | 884 | 884 | 0.091% | 100% | - | - | - |
| Ont-MT1 | 578,886 | 18,079 | 18,079 | 3.1% | 100% | - | - | - |
| Ont-MT2 | 541,022 | 8,594 | 8,594 | 1.6% | 100% | - | - | - |
| BC-22 | 133,568 | 35,374 | 6,036 | 4.5% | 17.1% | 29,337 | - | 1 baculovirus |
| BC-44 | 143,907 | 67,448 | 1,824 | 1.3% | 2.7% | 65,624 | - | - |
| BC-59 | 110,049 | 2,751 | 18 | 0.016% | 0.65% | 2,730 | - | 3 HERV |
| BC-76 | 148,434 | 4,871 | 4,835 | 3.3% | 99.3% | 6 | - | 26 adenovirus type 4; 2 ebola virus; 2 sweet potato chlorotic stunt virus |
| Mex-619 | 1,972,432 | 1,050 | 938 | 0.048% | 89.3% | 111 | 1 | - |
| Mex-730 | 86,070 | 81 | 78 | 0.091% | 96.3% | 3 | - | - |
| Mex-943 | 466,334 | 433 | 415 | 0.089% | 95.8% | 16 | 2 | - |
| Mex-956 | 193,452 | 19 | 6 | 0.0031% | 31.6% | 5 | - | 8 HERV |
| Mex-1225 | 905,314 | 21 | 10 | 0.0011% | 47.6% | 10 | - | 1 iridovirus (rice virus) |
| Cal-UC2 | 747,965 | 54,081 | 53,671 | 7.2% | 99.2% | 393 | 5 | 12 baculovirus |
| Cal-UC6 | 201,808 | 23,516 | 21,937 | 10.9% | 93.3% | 1,571 | 8 | - |
| Cal-UC12 | 2,042,430 | 274 | 270 | 0.013% | 98.5% | 4 | - | - |
| TOTAL | 9,819,120 | 222,368 | 122,487 | 1.2% | 55.1% | 99,810 | 16 | 55 |
Abbreviations: Orthomyxo, orthomyxovirus; MLV, murine leukemia virus; HERV, human endogenous retrovirus.