Junction characteristics of identified rearrangements, one case was only detected in T2T
| Sample ID | BPJs | ChrA | posA | ChrB | posB | Strand | Gene posA | Gene posB | Breakpoint insertions (nt) | Repeat A | Repeat B | Microhomology (nt) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GRCh38 (hg38) | ||||||||||||
| P1 | 1 | 4 | 181414917 | 9 | 13043905 | +/− | – | – | – | L1 | L1 | – |
| 1 | 16 | 28455071 | 16 | 29476612 | +/+ | – | – | – | AluJo | SVA_D | – | |
| P3 | 2 | 22 | 50618055 | 22 | 50624868 | +/− | – | ARSA | 2 | tigger1 | MIR | – |
| 22 | 50624361 | 22 | 50626277 | +/− | ARSA | ARSA | – | Alusp | – | 2 | ||
| P4 | 4 | 2 | 5549092 | 2 | 5858296 | +/− | XR_001739261.1 | – | – | – | L1PA7 | 4 |
| 2 | 5620671 | 2 | 7241289 | +/+ | – | – | 9 | – | – | – | ||
| 2 | 6246303 | 2 | 7734100 | +/+ | – | – | – | L1M5 | – | 2 | ||
| 2 | 6248808 | 2 | 7246507 | +/− | – | – | – | L1ME4b | – | 3 | ||
| 2 | 2 | 132954122 | 2 | 137703180 | +/− | NCKAP5 | – | – | MLT1K | L1PA16 | 1 | |
| 2 | 133434126 | 2 | 141163928 | +/− | NCKAP5 | LRP1B | – | – | 11 | |||
| P5 | 5 | 3 | 54518907 | 3 | 63614153 | +/− | CACNA2D3 | SYNPR | – | – | MamRep38 | – |
| 3 | 59407900 | 3 | 135767535 | +/− | XR_002959675.1 | – | – | – | MER101 | 1 | ||
| 3 | 63614153 | 3 | 145600155 | +/− | SYNPR | – | – | MamRep38 | L2A | – | ||
| 3 | 80981660 | 3 | 135891958 | +/− | – | – | – | MSTA-int | L2a | 1 | ||
| 3 | 80981660 | 3 | 148110490 | +/+ | – | – | 1 | MSTA-int | MER58A | – | ||
| P6 | 2 | 9 | 97596764 | X | 153779639 | +/− | TMOD1 | – | – | – | – | 1 |
| 9 | 97598236 | X | 153724706 | +/− | TMOD1 | BCAP31 | 12 | AluSX1 | – | – | ||
| P7.1 P7.3 | 4 | 1 | 19783172 | 10 | 95395335 | +/− | TMCO4 | SORBS1 | 7 | MIRb | – | – |
| 1 | 19783105 | 10 | 95395328 | +/− | TMCO4 | SORBS1 | 5 | MIRb | – | – | ||
| 2 | 189694535 | 2 | 202576085 | +/− | – | ANKAR | 1 | – | L1PA17 | – | ||
| 2 | 189694533 | 2 | 202576083 | +/− | – | ANKAR | – | – | L1PA17 | 1 | ||
| P8.1 P8.2 | 2 | X | 9420014 | X | 154113037 | +/− | XR_001755796.1 | – | 28 | AluJr | AluSx1 | – |
| X | 9768909 | X | 154208530 | +/− | GPR143 | – | 31 | AluSz6 | AluJo | – | ||
| P11 | 1 | X | 55349282 | X | 101431831 | +/− | – | ARMCX4 | – | AluY | AluY | 290 |
| P12 | 5 | 4 | 80390384 | 6 | 20052376 | +/− | CFAP299 | – | – | L1MA9 | AluSq2 | 1 |
| 4 | 94218568 | 6 | 20052374 | +/− | SMARCAD1 | – | – | AluSz | AluSq2 | 1 | ||
| 1 | 58205787 | 4 | 106505089 | +/− | DAB1 | – | – | – | THE1D | – | ||
| 1 | 58205785 | 4 | 106505092 | +/− | DAB1 | – | – | – | THE1D | 2 | ||
| 6 | 48002694 | 6 | 49160076 | +/+ | PTCHD4 | – | – | L1PA4 | – | 3 | ||
| T2T | ||||||||||||
| P9 | 2 | 9 | 75862011a | X | 3044233 | +/− | – | – | – | (AATGG)n | ERVL-MaLR | 2 |
| 9 | 75862011a | X | 3044228 | +/− | – | – | 990 | (TTCCA)n | ERVL-MaLR | – | ||
[i] (BPJ) breakpoint junction, (Chr) Chromosome, (pos) position, (nt) nucleotide; bold text indicates a disease-causing gene.
[ii] aEstimated location.