Table 4.
Partial comparison of the proportion and detailed classification of detected repeats generated based on two databases of the Glycine max genome
| Combination of RepBase and Dfam [bases masked: 36.11%] | msRepDB [bases masked: 41.54%] | |||||
|---|---|---|---|---|---|---|
| Repeat types | Number of elements | Length occupied | Percentage of sequences | Number of elements | Length occupied | Percentage of sequences |
| Retroelements | 199 220 | 289 032 002 bp | 29.52% | 244 764 | 328 295 871 bp | 33.54% |
| +SINEs | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +Penelope | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +LINEs | 12 626 | 10 304 690 bp | 1.05% | 13 156 | 10 432 965 bp | 1.07% |
| ++CRE/SLACS | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++L2/CR1/Rex | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++R1/LOA/Jockey | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++R2/R4/NeSL | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +++RTE/Bov-B | 3 790 | 2 001 199 bp | 0.20% | 3 945 | 2 017 968 bp | 0.21% |
| +++L1/CIN4 | 8 836 | 8 303 491 bp | 0.85% | 9 211 | 8 414 997 bp | 0.86% |
| +LTR elements | 186 594 | 278 727 312 bp | 28.47% | 231 608 | 317 862 906 bp | 32.47% |
| ++BEL/Pao | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| ++Tyl/Copia | 58 199 | 80 563 666 bp | 8.23% | 83 194 | 87 429 549 bp | 8.93% |
| ++Gypsy/DTRS1 | 126 690 | 195 309 037 bp | 19.95% | 140 926 | 225 546 399 bp | 23.04% |
| +++Retroviral | 0 | 0 bp | 0.00% | 340 | 206 126 bp | 0.02% |
| DNA transposons | 58 468 | 41 514 301 bp | 4.24% | 61 139 | 42 789 484 bp | 4.37% |
| +hobo-Activator | 7 612 | 2 233 822 bp | 0.23% | 5 901 | 1 964 869 bp | 0.20% |
| +Tc1-IS630-Pogo | 117 | 56 379 bp | 0.01% | 321 | 75 504 bp | 0.01% |
| +En-Spm | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +MuDR-IS905 | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +PiggyBac | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| +Tourist/Harbinger | 923 | 564 171 bp | 0.06% | 1 006 | 582 191 bp | 0.06% |
| +Other | 0 | 0 bp | 0.00% | 0 | 0 bp | 0.00% |
| Rolling circles | 538 | 252 405 bp | 0.03% | 967 | 740 481 bp | 0.08% |
| Unclassified | 0 | 0 bp | 0.00% | 46 116 | 9 214 511 bp | 0.94% |
| Total interspersed repeats | 330 546 303 bp | 33.77% | 378 050 943 bp | 38.62% | ||
| Small RNA | 2 223 | 902 022 bp | 0.09% | 2 221 | 901 834 bp | 0.09% |
| Satellites | 19 885 | 2 175 759 bp | 0.22% | 9 389 | 6 367 996 bp | 0.65% |
| Simple repeats | 323 670 | 15 236 633 bp | 1.56% | 307 769 | 14 416 738 bp | 1.47% |
| Low complexity | 82 139 | 4 344 053 bp | 0.44% | 75 689 | 3 964 123 bp | 0.40% |
The test results were obtained by using RepeatMasker based on the msRepDB database and the combination of Dfam and RepBase respectively under the default parameter settings.