Table 4.
Features and diversity of TE models found in the galGal4 model based on the REPET and DM annotations (STEP3 + STEP4, Fig. 2) after stack resolving and merging stacked and juxtaposed annotations
| Names of TE models | a | b | ca | d | e |
|---|---|---|---|---|---|
| CR1 | 308 | LINE | 413857 | 66.4707 | 11.8457 |
| Ancestral_LTR_group_1 | 3 | LTR | 86 | 0.0138 | 0.0034 |
| Ancestral_LTR_group_2 | 1 | LTR | 22 | 0.0035 | 0.0013 |
| Ancestral_LTR_group_3 | 1 | LTR | 40 | 0.0064 | 0.0012 |
| Ancestral_LTR_group_4 | 1 | LTR | 308 | 0.0495 | 0.0119 |
| BIRDDAWG | 10 | LTR | 6238 | 1.0019 | 0.2525 |
| EAV | 1 | LTR | 191 | 0.0307 | 0.0212 |
| EAV-HP | 7 | LTR | 765 | 0.1229 | 0.0496 |
| ERV2 | 2 | LTR | 426 | 0.0684 | 0.0209 |
| ERV7 | 10 | LTR | 2885 | 0.4634 | 0.1061 |
| ERV11 | 1 | LTR | 512 | 0.0822 | 0.0168 |
| Kronos | 46 | LTR | 30732 | 4.9359 | 0.7377 |
| putative_LTR_group4 | 2 | LTR | 835 | 0.1341 | 0.0137 |
| putative_LTR_group9 | 1 | LTR | 170 | 0.0273 | 0.0017 |
| putative_LTR_group12 | 17 | LTR | 1797 | 0.2886 | 0.05 |
| putative_LTR_group22 | 3 | LTR | 1219 | 0.1958 | 0.0257 |
| putative_LTR_group28 | 2 | LTR | 367 | 0.0589 | 0.0116 |
| putative_LTR_group30 | 13 | LTR | 3847 | 0.6179 | 0.0996 |
| retroCalimero | 1 | LTR | 826 | 0.1327 | 0.0540 |
| retroSaturnin | 1 | LTR | 161 | 0.0259 | 0.0118 |
| retroTux | 2 | LTR | 2490 | 0.3999 | 0.1243 |
| Soprano | 19 | LTR | 3014 | 0.4841 | 0.1171 |
| Charlie | 3 | TIR | 37319 | 5.9939 | 0.5868 |
| Charlie-Galluhop | 5 | TIR | 67691 | 10.872 | 1.0296 |
| Galluhop | 2 | TIR | 4588 | 0.7369 | 0.1198 |
| Mariner1_GG | 10 | TIR | 5686 | 0.9132 | 0.1491 |
| Hitchcock | 4 | undefined | 27033 | 4.3418 | 0.4182 |
| undetermined_group_1 | 3 | undefined | 2219 | 0.3564 | 0.0773 |
| undetermined_group_2 | 2 | undefined | 1030 | 0.1654 | 0.0165 |
| undetermined_group_3 | 2 | undefined | 174 | 0.0279 | 0.0045 |
| undetermined_group_4 | 4 | undefined | 2550 | 0.4096 | 0.0423 |
| undetermined_group_5 | 2 | undefined | 134 | 0.0215 | 0.0036 |
| undetermined_group_6 | 1 | undefined | 372 | 0.0597 | 0.0100 |
| Z_rep | 9 | undefined | 3032 | 0.487 | 0.1476 |
| Total | 499 | 622616 | 100 | 16.1832b |
a, Number of consensus; b, TE types; c, Total number of TE copies; d, Percentage of the total number of TE copies; e, Percentage of chromosome coverage; aPost stack resolving and annotation merging are called copies all complete elements, internally deleted elements; 5' or 3' truncated elements and elements truncated at both ends (i.e. internal regions of a TE devoid of ends). bthis coverage value was more elevated than the 15.7 % indicated in the main text because the coverage corresponding to the small TE copies nested in larger TEs were not removed for these calculations