Table 5. Post-alignment QAQC using Bowtie2 of the unaligned reads from Tophat2.
| Sample name | Total reads | Aligned (%) | Unique (%) | Coverage (%) | Avg. coverage depth | Avg. length | Avg. quality | Avg. mapping quality | % GC |
| pcDNA3 | 2,202,603 | 96.89 | 96.89 | 1.23 | 5.05 (SD 37.81) | 126.77 | 27.43 | 19.60 (SD 14.41) | 51.53 |
| HEV1 | 2,498,488 | 96.48 | 96.48 | 1.33 | 5.99 (SD 182.52) | 135.69 | 27.3 | 21.09 (SD 14.53) | 54.73 |
| HEV2 | 3,604,321 | 97.67 | 97.67 | 1.56 | 7.08 (SD 64.82) | 136.02 | 25.73 | 19.33 (SD 14.38) | 52.24 |
| HBV1 | 3,159,660 | 95.31 | 95.31 | 1.30 | 8.08 (SD 437.10) | 138.52 | 25.15 | 19.95 (SD 13.88) | 55.29 |
| HBV2 | 2,489,732 | 95.97 | 95.97 | 1.27 | 5.47 (SD 62.75) | 123.05 | 26.39 | 20.21 (SD 14.58) | 52.30 |
| HBVHEV1 | 1,625,785 | 88.73 | 88.73 | 0.96 | 4.02 (SD 119.93) | 104.59 | 26.51 | 22.98 (SD 14.97) | 54.50 |
| HBVHEV2 | 2,665,864 | 95.58 | 95.58 | 1.28 | 6.38 (SD 78.35) | 135.24 | 25.84 | 19.99 (SD 14.51) | 52.37 |