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. 2018 Jul 18;9:1577. doi: 10.3389/fmicb.2018.01577

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.