Table 2. Repeat annotations are more refined for CHM13v1.1.
Kilo–base pairs of repeat annotations, by repeat class and family, for different human genome assemblies with T2T-CHM13v1.1 RMv2, GRCh38 RMv2, and GRCh38 Dfam3.3 only. Note that AluJb is included in the Alu repeat family category.
| Repeat class | Repeat family | CHM13v1.1 |
GRCh38 (excluding Y) |
||||
|---|---|---|---|---|---|---|---|
| RMv2 |
RMv2 |
Dfam3.3 |
|||||
| Kbp | % of assembly | Kbp | % of assembly | Kbp | % of assembly | ||
| SINE | 5S-Deu-L2 | 221.0 | 0.0072 | 218.2 | 0.0075 | 210.9 | 0.0072 |
| Alu | 308,309.7 | 10.0926 | 304,734.4 | 10.4283 | 305,457.4 | 10.4531 | |
| MIR | 80,937.9 | 2.6495 | 80,726.2 | 2.7625 | 79,989.0 | 2.7373 | |
| tRNA-Deu | 48.4 | 0.0016 | 48.1 | 0.0016 | 46.1 | 0.0016 | |
| tRNA-RTE | 549.0 | 0.0180 | 546.9 | 0.0187 | 525.9 | 0.0180 | |
| tRNA | 1.6 | 0.0066 | 1.6 | 0.0069 | 1.5 | 0.0067 | |
| Retroposon | SVA | 4,654.7 | 0.1524 | 4,507.8 | 0.1543 | 4,520.7 | 0.1547 |
| LINE | CR1 | 10,817.9 | 0.3541 | 10,805.0 | 0.3698 | 10,571.1 | 0.3618 |
| Dong-R4 | 120.1 | 0.0039 | 121.0 | 0.0041 | 115.2 | 0.0039 | |
| I-Jockey | 15.7 | 0.0005 | 15.6 | 0.0005 | 14.8 | 0.0005 | |
| L1 | 512,421.5 | 16.7742 | 507385.6 | 17.3633 | 507,866.7 | 17.3797 | |
| L1-Tx1 | 49.6 | 0.0016 | 50.3 | 0.0017 | 49.1 | 0.0017 | |
| L2 | 104,083.4 | 3.4072 | 103,819.6 | 3.5528 | 102,055.0 | 3.4924 | |
| RTE-BovB | 872.7 | 0.0286 | 875.3 | 0.0300 | 843.2 | 0.0289 | |
| RTE-X | 3,195.6 | 0.1046 | 3,190.0 | 0.1092 | 3,097.8 | 0.1060 | |
| Penelope | 68.0 | 0.0022 | 68.4 | 0.0023 | 63.1 | 0.0022 | |
| LTR | ERV1 | 83,480.5 | 2.7327 | 82,370.2 | 2.8188 | 82,641.0 | 2.8281 |
| ERVK | 8,611.5 | 0.2819 | 8,370.9 | 0.2865 | 8,468.0 | 0.2898 | |
| ERVL | 59,049.8 | 1.9330 | 58,682.4 | 2.0082 | 58,646.0 | 2.0069 | |
| ERVL-MaLR | 110,751.8 | 3.6255 | 110,098.6 | 3.7677 | 109,957.5 | 3.7629 | |
| Gypsy | 4,843.6 | 0.1586 | 4,826.3 | 0.1652 | 4,629.3 | 0.1584 | |
| Undefined | 3,172.7 | 0.1039 | 3,176.1 | 0.1087 | 3,081.7 | 0.1055 | |
| DNA | Crypton | 44.4 | 0.0015 | 45.1 | 0.0015 | 44.5 | 0.0015 |
| Crypton-A | 21.7 | 0.0007 | 22.0 | 0.0008 | 20.6 | 0.0007 | |
| Kolobok | 65.7 | 0.0021 | 65.7 | 0.0022 | 63.9 | 0.0022 | |
| MULE-MuDR | 1,008.0 | 0.0330 | 985.5 | 0.0337 | 986.8 | 0.0338 | |
| Merlin | 40.3 | 0.0013 | 40.6 | 0.0014 | 40.0 | 0.0014 | |
| PIF-Harbinger | 68.5 | 0.0022 | 70.0 | 0.0024 | 67.6 | 0.0023 | |
| PiggyBac | 540.6 | 0.0177 | 541.4 | 0.0185 | 539.5 | 0.0185 | |
| TcMar | 44.9 | 0.0015 | 45.5 | 0.0016 | 45.2 | 0.0015 | |
| TcMar-Mariner | 2,961.4 | 0.0969 | 2,888.2 | 0.0988 | 2,872.1 | 0.0983 | |
| TcMar-Pogo | 4.5 | 0.0001 | 4.2 | 0.0001 | 4.0 | 0.0001 | |
| TcMar-Tc1 | 135.8 | 0.0044 | 135.8 | 0.0046 | 134.1 | 0.0046 | |
| TcMar-Tc2 | 1,678.1 | 0.0549 | 1,666.6 | 0.0570 | 1,665.6 | 0.0570 | |
| TcMar-Tigger | 37,999.9 | 1.2439 | 37,725.0 | 1.2910 | 37,557.8 | 1.2853 | |
| hAT | 561.8 | 0.0184 | 561.6 | 0.0192 | 543.1 | 0.0186 | |
| hAT-Ac | 653.4 | 0.0214 | 634.7 | 0.0217 | 610.5 | 0.0209 | |
| hAT-Blackjack | 2,608.8 | 0.0854 | 2,603.9 | 0.0891 | 2,589.8 | 0.0886 | |
| hAT-Charlie | 46,980.9 | 1.5379 | 46,779.6 | 1.6008 | 46,468.2 | 1.5902 | |
| hAT-Tag1 | 476.1 | 0.0156 | 476.5 | 0.0163 | 463.2 | 0.0159 | |
| hAT-Tip100 | 12,250.5 | 0.4010 | 12,034.5 | 0.4118 | 11,915.0 | 0.4077 | |
| hAT-hAT19 | 1.8 | 0.0001 | 1.7 | 0.0001 | 1.6 | 0.0001 | |
| Undefined | 1,201.8 | 0.0393 | 1,202.9 | 0.0412 | 1163.1 | 0.0398 | |
| Kilo–base pairs of TEs | 1,405,826.3 | 1,393,370.3 | 1,390,841.6 | ||||
| Kilo–base pairs of non-TEs | 241,986.3 | 122,998.7 | 118,576.2 | ||||
| Assembled kilo–base pairs | 3,054,815.5 | 2,922,175.7 | 2,922,175.7 | ||||
| TEs masked | 46.02 | 47.68 | 47.60 | ||||
| Non-TEs masked | 7.92 | 4.21 | 4.06 | ||||
| % repeatmasked | 53.941 | 51.892 | 51.654. | ||||