Table 2 Repeats in putative misassembly regions compared to the whole genome
Repetitive element | O_niloticus_UMD1 genome wide | Within 34 misassembly regions | Enrichment | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Order | Family | # | Total bp | % | Mean length | # | Total bp | % | Mean length | Ratio of genome/missassem regions | Δ mean length |
DNA | Sola | 7,007 | 1,536,337 | 0.15% | 219.3 | 142 | 53,045 | 1.37% | 373.6 | 913.3% | 154.3 |
TcMar-Tc1 | 156,588 | 46,394,192 | 4.60% | 296.3 | 846 | 354,606 | 9.18% | 419.2 | 199.6% | 122.9 | |
hAT | 36,441 | 10,103,158 | 1.00% | 277.2 | 289 | 99,016 | 2.56% | 342.6 | 256.0% | 65.4 | |
hAT-Ac | 49,528 | 17,626,929 | 1.75% | 355.9 | 445 | 191,054 | 4.95% | 429.3 | 282.9% | 73.4 | |
hAT-Charlie | 37,049 | 13,709,558 | 1.36% | 370.0 | 236 | 99,913 | 2.59% | 423.4 | 190.4% | 53.3 | |
LINE | L1 | 10,712 | 8,879,041 | 0.88% | 828.9 | 63 | 79,410 | 2.06% | 1,261 | 234.1% | 431.6 |
L2 | 76,937 | 29,334,193 | 2.91% | 381.3 | 539 | 269,645 | 6.98% | 500.3 | 239.9% | 119.0 | |
Penelope | 28,509 | 7,214,522 | 0.71% | 253.1 | 258 | 70,627 | 1.83% | 273.7 | 257.7% | 20.7 | |
Rex-Babar | 38,996 | 19,208,630 | 1.90% | 492.6 | 386 | 199,730 | 5.17% | 517.4 | 272.1% | 24.9 | |
LTR | ERV1 | 10,756 | 6,450,995 | 0.64% | 599.8 | 112 | 97,055 | 2.51% | 866.6 | 392.2% | 266.8 |
Gypsy | 29,201 | 13,615,743 | 1.35% | 466.3 | 274 | 172,231 | 4.46% | 628.6 | 330.4% | 162.3 | |
RC | Helitron | 3,882 | 2,685,111 | 0.27% | 691.7 | 216 | 187,805 | 4.86% | 869.5 | 1800.0% | 177.8 |
Unk. | Unknown | 350,007 | 97,456,302 | 9.66% | 278.4 | 2,188 | 841,264 | 21.78% | 384.5 | 225.5% | 106.0 |
Satellite | Satellite | 10,061 | 7,662,597 | 0.76% | 761.6 | 93 | 115,309 | 2.99% | 1,240 | 393.4% | 478.3 |
Simple | 322,732 | 15,543,664 | 1.54% | 48.2 | 1,733 | 173,824 | 4.50% | 100.3 | 292.2% | 52.1 | |