Table 7 Repetitive element summary
From: An improved genome reference for the African cichlid, Metriaclima zebra
M_zebra_v0 | M_zebra_UMD1 | Δ from M_zebra_v0 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
order | super-family | number | bp | mean bp size | median bp size | number | bp | mean bp size | median bp size | number | bp | mean bp size | median bp size |
DNA | TcMar-Tc1 | 133,563 | 30,394,950 (−3.58 %) | 227.6 | 152 | 137,896 | 40,100,895 (4.66 %) | 290.8 | 173 | 4,333 | 9,705,945 | 63.2 | 21 |
hAT-Ac | 41,018 | 9,251,093 (1.09 %) | 225.5 | 143 | 43,310 | 16,553,134 (1.93 %) | 382.2 | 215 | 2,292 | 7,302,041 | 156.7 | 72 | |
LINE | L1 | 9,184 | 3,265,323 (0.38 %) | 355.5 | 190 | 11,186 | 7,488,720 (0.87 %) | 669.5 | 318.5 | 2,002 | 4,223,397 | 313.9 | 128.5 |
L2 | 65,651 | 14,708,900 (1.73 %) | 224.0 | 148 | 62,048 | 18,525,102 (2.15 %) | 298.6 | 168 | −3,603 | 3,816,202 | 74.5 | 20 | |
Rex-Babar | 25,685 | 6,087,899 (0.72 %) | 237.0 | 139 | 30,109 | 14,508,668 (1.69 %) | 481.9 | 202 | 4,424 | 8,420,769 | 244.8 | 63 | |
LTR | Gypsy | 10,865 | 3,908,793 (0.46 %) | 359.8 | 159 | 14,026 | 6,476,548 (0.75 %) | 461.8 | 184 | 3,161 | 2,567,755 | 102.0 | 25 |
Ngaro | 3,955 | 393,178 (0.05 %) | 99.4 | 94 | 10,633 | 1,841,475 (0.21 %) | 173.2 | 157 | 6,678 | 1,448,297 | 73.8 | 63 | |
SINE | MIR | 12,756 | 1,741,837 (0.21 %) | 136.6 | 111 | 10,900 | 2,395,459 (0.28 %) | 219.8 | 165 | −1,856 | 653,622 | 83.2 | 54 |
tRNA-Core | 7,419 | 953,921 (0.11 %) | 128.6 | 124 | 12,054 | 1,819,302 (0.21 %) | 150.9 | 145 | 4,635 | 865,381 | 22.4 | 21 | |
Unknown | 285,700 | 49,619,702 (5.85 %) | 173.7 | 126 | 279,557 | 58,688,408 (6.83 %) | 209.9 | 138 | −6,143 | 9,068,706 | 36.3 | 12 | |
Ancestral repeats | 1,101,882 | 173,081,089 (20.39 %) | 1,153,935 | 234,447,039 (27.27 %) | 61,365,950 | ||||||||
Lineage specific | 17,320 | 4,748,554 (0.56 %) | 15,585 | 6,875,733 (0.80 %) | 2,127,179 | ||||||||
Total | 1,119,202 | 177,829,643 (20.95 %) | 1,169,520 | 241,322,772 (28.07 %) | 63,493,129 | ||||||||