Table 2.
Distribution of PR and RT search results in the human genome GRCh38.
| Chromosome | tBLASTn ERVK-10 PR | LTRdigest RVP | tBLASTn Phoenix RVT_1 | LTRdigest RVT_1 | ||
|---|---|---|---|---|---|---|
| Raw | Curated | Raw | Curated | |||
| 1 | 32 | 15 | 97 | 34 | 115 | 15 |
| 2 | 17 | 6 | 79 | 36 | 95 | 7 |
| 3 | 28 | 14 | 109 | 57 | 136 | 13 |
| 4 | 35 | 14 | 113 | 53 | 144 | 15 |
| 5 | 23 | 11 | 74 | 39 | 140 | 9 |
| 6 | 30 | 6 | 95 | 37 | 104 | 9 |
| 7 | 18 | 3 | 58 | 24 | 92 | 3 |
| 8 | 24 | 13 | 91 | 32 | 85 | 13 |
| 9 | 8 | 1 | 39 | 13 | 49 | 3 |
| 10 | 19 | 5 | 52 | 23 | 80 | 8 |
| 11 | 18 | 12 | 71 | 40 | 104 | 12 |
| 12 | 15 | 10 | 75 | 37 | 82 | 10 |
| 13 | 5 | 2 | 34 | 19 | 30 | 1 |
| 14 | 10 | 4 | 35 | 13 | 57 | 4 |
| 15 | 7 | 3 | 17 | 7 | 26 | 3 |
| 16 | 10 | 4 | 23 | 12 | 14 | 2 |
| 17 | 11 | 3 | 21 | 17 | 10 | 2 |
| 18 | 2 | 3 | 19 | 5 | 28 | 2 |
| 19 | 42 | 6 | 76 | 38 | 18 | 6 |
| 20 | 5 | 0 | 15 | 0 | 20 | 0 |
| 21 | 3 | 0 | 12 | 6 | 10 | 0 |
| 22 | 7 | 1 | 14 | 6 | 12 | 1 |
| X | 22 | 7 | 108 | 14 | 267 | 7 |
| Y | 37 | 7 | 85 | 10 | 48 | 4 |
| Alternative | 52 | N/A | 64 | N/A | N/A | N/A |
| Total | 480 | 150 | 1412 | 572 | 1766 | 149 |
“Raw” refers to all sequences identified, and “Curated” refers only to sequences that were aligned for further analysis. Credible RT sequences are those which were not eliminated for causing gappy sites. Curated RVT_1 sequences are those which co-occurred with another retroviral HMM match. LTRharvest and LTRdigest were not used to search alternative assemblies, so there are no results to report. Since this curation workflow did not exclude any protease search results, the number is shown only once.