Table 5. Deletion- type DVGs identified in viruses #1 and #2 using DVG-profiler.
| Rescue | Reads found with deletion (no. of reads in repeat HiSeq run)a | Breakpoint/Reinitiation position | Size of deletion (nt) | Ratio DVG / full-length genome c |
|---|---|---|---|---|
|
1 |
281 (N/A) | 13814 / 14707 | 893 | 0.014 (N/A) |
| 179 (N/A) | 12274 / 14422 | 2148 | 0.003 (N/A) | |
| 119 (N/A) | 5163 / 10845 | 5682 | 0.002 (N/A) | |
|
2 |
62570 (70986) | 14589 / 15046b | 457 | 2.6 (2.36) |
| 2015 (1276) | 14960 / 15166 | 207 | 0.08 (0.04) | |
| 2009 (949) | 13916 / 15284 | 1368 | 0.08 (0.03) | |
| 1079 (1069) | 5785 / 15175 | 9390 | 0.04 (0.03) | |
| 665 (1159) | 6249 / 14475 | 8226 | 0.028 (0.04) | |
| 490 (753) | 4175 / 13739 | 9564 | 0.02 (0.025) | |
| 304 (242) | 14949 / 15155 | 206 | 0.012 (0.008) | |
| 296 (288) | 14365 / 14881 | 516 | 0.012 (0.01) | |
| 244 (246) | 2422 / 13755 | 11333 | 0.01 (0.008) | |
| 219 (241) | 14365 / 14693 | 328 | 0.01 (0.008) | |
| 200 (398) | 812 / 13431 | 12619 | 0.008 (0.013) | |
| 181 (78) | 14457 / 14885 | 428 | 0.008 (0.003) | |
| 169 (127) | 11443 / 15171 | 3728 | 0.007 (0.004) | |
| 169 (121) | 3196 / 12185 | 8989 | 0.007 (0.004) | |
| 168 (209) | 2127 / 10975 | 8848 | 0.006 (0.007) | |
| 140 (128) | 5029 / 12136 | 7107 | 0.005 (0.004) | |
| 111 (27) | 14890/ 15029 | 139 | 0.005 (0.001) | |
| 110 (37) | 13315 / 14875 | 1560 | 0.004 (0.001) | |
| 106 (146) | 1896 / 14927 | 13031 | 0.004 (0.005) | |
| 106 (89) | 2294 / 14177 | 11883 | 0.004 (0.003) |
a Listed are all deletion- type DVGs identified with 100 or more reads.
b This deletion was detected in copyback DVGs 13907/15279 and 14223/15166 using primer pair a/b3 (see Table 1). In addition, the existence of the deletion was confirmed by conventional RT-PCR using primers b6 and a that are flanking the deletion.
c The ratios were calculated based on average estimated coverages of 62550, 24000 and 30062 reads for full-length genomes in viruses #1, #2, and virus #2 (repeat run), respectively
N/A not applicable