Table 5. Number and location of nonreference TEs predicted by McClintock component methods in 93 yeast genomes.
| Carr | ngs_te_mapper | RelocaTE | TEMP | RetroSeq | PoPoolationTE | TE-locate | |
|---|---|---|---|---|---|---|---|
| Ty1 | 218/313 (70%) | 93/101 (92%) | 15/18 (83%) | 827/1093 (76%) | 1854/2835 (65%) | 139/194 (72%) | 2082/16388 (13%) |
| Ty2 | 30/46 (65%) | 58/77 (75%) | 303/425 (71%) | 1343/1853 (72%) | 839/1169 (72%) | 27/36 (75%) | 1110/8132 (14%) |
| Ty3 | 43/45 (96%) | 378/387 (98%) | 670/678 (99%) | 991/1008 (98%) | 1299/1445 (90%) | 1006/1013 (99%) | 1748/3813 (46%) |
| Ty3_1p | 12/15 (80%) | 0/0 (N.A.) | 23/23 (100%) | 0/0 (N.A.) | 12/16 (75%) | 0/0 (N.A.) | 83/86 (97%) |
| Ty4 | 29/49 (59%) | 95/118(81%) | 143/190(75%) | 259/310(84%) | 238/292(82%) | 15/20(75%) | 324/1083(30%) |
| Ty5 | 0/15 (0%) | 0/0 (N.A.) | 0/0 (N.A.) | 0/0 (N.A.) | 3/74 (4%) | 0/12 (0%) | 0/887 (0%) |
Each cell shows the number of nonreference TEs predicted in tRNA regions followed by the total number of nonreference TEs predicted genome wide. Data are for numbers of insertions, not numbers of nonredundant insertion sites, so TE insertion alleles present in more than one sample are counted independently. A prediction is counted in a tRNA region if any portion of the annotation is within 1000 bp upstream and 500 bp downstream of the tRNA start site, taking into account the orientation of the tRNA gene. The first column applies the same analysis to the reference TE annotations from Carr et al. (2012). N.A. indicates that no nonreference TE insertions were predicted by a method for that TE family.