Table 2.
NGS analysis of encapsidated DNA
| Target aligned against | Filter step | Bac-RepCap | SGMO Helper | Bac-RepCap | SGMO Helper |
|---|---|---|---|---|---|
| Input vector genome | 0 | 94.5 | 94.1 | 98.7 | 92.3 |
| Kanamycin resistance gene | 1 | 0.008 | 0.000 | 0.000 | 0.000 |
| Gentamicin resistance gene | 2 | 0.004 | 0.000 | 0.000 | 0.000 |
| Bacmid with F9 cDNA vector genome | 3 | 1.998 | 0.758 | 0.163 | 0.820 |
| pRep2Cap1 | 4 | 0.023 | 0.000 | 0.010 | 0.011 |
| pRep2Cap2 | 5 | 0.000 | 0.000 | 0.000 | 0.000 |
| pRep2Cap5 | 6 | 0.000 | 0.000 | 0.000 | 0.000 |
| pRep2Cap6 | 7 | 0.002 | 0.000 | 0.000 | 0.000 |
| pRep2Cap8 | 8 | 0.000 | 0.000 | 0.000 | 0.000 |
| pRep2Cap8_Kan | 9 | 0.000 | 0.000 | 0.000 | 0.000 |
| pRep2Cap9 | 10 | 0.000 | 0.000 | 0.000 | 0.000 |
| pRepCap3B | 11 | 0.000 | 0.008 | 0.000 | 0.000 |
| Sf9 genome (FDA) | 12 | 0.076 | 0.032 | 0.010 | 0.063 |
| Transfer vector with F9 cDNA vector genome | 13 | 0.002 | 0.000 | 0.000 | 0.000 |
| Empty transfer vector | 14 | 0.000 | 0.000 | 0.000 | 0.000 |
| pMON7124 (transposase plasmid) | 15 | 0.008 | 0.072 | 0.004 | 0.000 |
| Plant rhabdovirus genome | 16 | 0.000 | 0.000 | 0.000 | 0.000 |
| phiX | 17 | 0.000 | 0.000 | 0.000 | 0.000 |
| Total mapped reads: | 96.654 | 95.000 | 98.893 | 93.165 | |
| Percentage of mapped reads that are vector genome: | 97.806 | 99.085 | 99.811 | 99.041 | |
| Percentage of unmapped reads: | 3.346 | 5.000 | 1.107 | 6.835 | |
Capsid-associated DNA was sequenced and mapped back to the vector genome or other potential contaminating sequences in sequential order, as indicated by the Filter Step. Values are presented as percentage of total sequences that mapped to a particular target. The percentage of mapped and unmapped reads is reported at the bottom of the table and the percentage of the total mapped reads that match the vector genome is also reported.