Table 3. Result of analysis for the three technique groups.
| Technique | SPEX | PEC | Hybridization capture | |||
|---|---|---|---|---|---|---|
| KoRV flanks orientation | 5 end | 3 end | 5 end | 3 end | 5 end | 3 end |
| KoRV flanks < 4 bp | 15,822 | 1,527 | 496 | 1,806 | 191 | 41 |
| KoRV flanks 4–14 | 6,426 | 8,896 | 329 | 2,033 | 1,052 | 24 |
| KoRV flanks 15 bp or longer | 95 | 304 | 63 | 314 | 106 | 4 |
| KoRV flanks > 4 bp | 6,521 | 9,200 | 392 | 2,347 | 1,158 | 28 |
| Unique insertion sites after clustering | 66 | 182 | 126 | 538 | 862 | 24 |
| Shared insertion sites after clustering | 15 | 28 | 17 | 134 | 25 | 0 |
| Internal KoRV reads | 212 | 223 | 141 | 1,406 | 151 | 14 |
| Total target enrichment products identified | 22,542 | 10,950 | 1,029 | 5,559 | 1,495 | 83 |
| Total sequences after PCR duplicate removal* | 714,929 | 1,188,365 | 11,675,245 | |||
| Efficiency of target enrichment (%) | 4.68 | 0.55 | 0.01 | |||
| Number of hits to wallaby genome by blast | 1,617 | 136,366 | 1,915,781 | |||
| Estimated ratio of off-target enrichment (%) | 0.23 | 11.48 | 16.41 | |||
Notes.
*
The total number of sequences after PCR duplicate removal equals the total number of sequences before pairwise alignment.