Features of rearrangements and breakpoints
| Haplotype | Rearrangement | NAHR SD pair | Breakpoint | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Class | Size (bp) | Length (kbp) | Identity (%) | Length (bp) | Identity (%) | Genes | Repetitive elements | GC content (%) | |
| H2.1 | Inversion | 1,433,448 | 446 | 99.46 | 17,420 | 99.80 | NPY4R | Large region | 49 |
| H2.2 | Inversion | 1,321,414 | 446 | 99.46 | 4993 | 99.64 | AC244230.2 | Large region | 48 |
| H2.3 | Inversion | 1,510,974 | 446 | 99.46 | 4999 | 99.84 | LINC00842 | Large region | 52 |
| H2.4 | Inversion | 993,568 | 446 | 99.46 | 25,598 | 99.89 | AL136982.3 | Large region | 39 |
| H2.5 | Inversion | 902,230 | 446 | 99.46 | 7220 | 99.74 | FAM245B | Large region | 36 |
| H3 | Deletion | 176,406 | 18 | 94.36 | 369 | 100 | No | No | 66 |
| H5 | Duplication | 714,524 | 56 | 99.15 | 867 | 100 | No | LINE L1M4 | 43 |
| H9 | Inversion | 1,089,232 | 68 | 99.20 | 1207 | 100 | ANXA8 | LINE L4_C_Mam | 51 |
| H10 | Deletion | 501,667 | 446 | 99.46 | 19,957 | 99.79 | FAM245B | Large region | 34 |
| H11 | Deletion | 671,796 | 122 | 99.63 | 1641 | 99.70 | FRMPD2 | LTR33 + MER20 | 52 |
[i] The length and identity of the entire SD pair mediating the NAHR event as well as features of the narrowed breakpoint sequence are shown. Data were taken from the CAT + Liftoff Gene Annotations, RepeatMasker Repetitive Elements, and GC Percent in 5-Base Windows UCSC Genome Browser tracks (T2T-CHM13 v2.0).