Characteristics of the resolved breakpoint junctions (BPJs) of marker and ring chromosomes, with coordinates mapped to the T2T-CHM13v2.0 genome build
| Case ID | sSMC | BPJ | Chr | PosA | PosB | Segment posA–posB | PosA: genes | PosB: genes | PosA: repeat | PosA: segmental duplication | PosB: segmental duplication | PosB: repeat | Microhomology (bp) | Insertion (bp) | Mechanism |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RD_P276 | r(5) | 1 | Chr 5 | 37,676,103 | 43,290,183 | A–B | WDR70, intron 5 | AC025171.1, intron 2 | LTR:MLT1H2 | — | — | Cent. | 3 | — | MMEJ |
| 2 | Chr 5 | 32,320,809 | 49,497,791a | A–B | — | — | LTR:MLT1F2 | — | — | Cent. | 3 | — | |||
| RD_P278 | r(7) | 1 | Chr 7 | 59,987,274 | 72,094,570 | A–B | — | — | Cent. | Yes | — | AluSx1 | — | 20 NT | MMBIR |
| 2 | Chr 7 | 59,978,281 | 59,987,351 | A–B | – | – | Cent. | Yes | Yes | Cent. | 3 | — | |||
| RD_P273 | r(8) | 1 | Chr 8 | 50,587,595 | 77,860,383 | A–B | SNTG1 | AC062004.1 | L1P1 | — | — | — | 2 | — | MMEJ |
| 2 | Chr 8 | 46,120,188a | 51,426,338 | A–B | — | — | Cent. | — | — | — | — | 4 (templated) | |||
| RD_P272 | r(9) | 1 | Chr 9 | 30,592,557 | 31,057,050 | B–C | — | — | — | — | — | L2c, L2a | — | 28 NT | MMBIR |
| 2 | Chr 9 | 28,144,043 | 31,568,556 | A–C | LINGO2, intron3 | — | L2d2 | — | — | L1P1 | — | 224 NT | |||
| 3 | Chr 9 | 29,574,524 | 91,174,804 | A–F | — | — | AluSx1 | — | — | — | 3 | — | |||
| 4 | Chr 9 | 39,306,747 | 91,060,755 | D–F | — | — | AluYk2, Satellite | Yes | — | MIRc | — | — | |||
| 5 | Chr 9 | 32,076,512 | 44,448,128 | D–E | — | ANKRD20A7P (pseudogene) | L1PB3 | — | Yes | Cent. | — | 100 NT | |||
| RD_P166 | r(13) | 1 | Chr 13 | 11,452,840 | 56,358,138 | A–C | — | PRR20C, intron 1 | Cent. | Yes | Yes | — | — | 42 (templated) | MMBIR |
| 2 | Chr 13 | 29,045,867 | 84,773,620 | B–C | UBL3, intron 1 | LINC00351, intron 1 | AluSp | — | — | — | — | — | |||
| RD_P550 | r(14) | 1 | Chr 14 | 9,208,604 | 16,434,843 | A–A | — | AC244502.1, TRA | Cent. | Yes | — | Cent., LTR/ERV1 | 2 | — | MMEJ |
| RD_P275 | r(20) | 1 | Chr 20 | 4,979,434 | 59,369,410 | A–C | SLC23A2, intron 2 | LOC102724968 | — | — | — | L2 | — | 205 (templated) | MMBIR |
| 2 | Chr 20 | 24,892,355 | 65,776,662 | B–C | — | UCKL1, intron 1 | Cent. | — | — | — | 7b | 2b | |||
| 3 | Chr 20 | 3,306,020 | 42,368,945 | A–B | DNAAF9/C20orf194/MSTRG | — | — | — | — | — | 4 | — | |||
| RD_P328 | der(7)t(X;7;5) | 1 | Chr 7-Chr 5 | Chr 7: 43,886,314 | Chr 5: 177,119,928 | A–B | COA1, intron 1 | CDHR2, exon 9 | L1MB8, AluYk2 | — | — | — | — | — | MMEJ |
| 2 | Chr X-Chr7 | Chr X: 14,614,119 | Chr 7: 75,313,264 | C–A | — | LIMK1, intron 10 | Simple repeats (AAAT) | — | — | AluJb | 3 | — | |||
| RD_P586 | der(X) | 1 | Chr X | 103,977,823 | 145,148,123 | F–J | IL1RAPL2, intron 6 | — | L2d, L1M4a1 | — | — | L1MA1 | 1 | — | MMBIR |
| 2 | Chr X | 89,566,572 | 89,651,697 | F–E | — | — | L1ME1 | — | Yes | L1ME3, ERVL-MaLR | — | — | |||
| 3 | Chr X | 66,181,028 | 84,675,390 | B–E | — | DACH2, intron 1 | L1ME3B | — | — | — | 2 | — | |||
| 4 | Chr X | 58,080,098 | 66,184,481 | A–B | NA | — | NA | — | — | LINE/L2a | 2 | — | |||
| 5 | Chr X | 74,310,915 | 144,750,571 | A–H | — | — | L1PA7, MLT2D, L1MEc | — | — | L1MA2, ERVL-MaLR | — | 1 | |||
| 6 | Chr X | 83,792,179 | 141,176,418 | D–H | POF1B, intron 3 | – | L1PREC2 | — | — | — | — | 37 NT (L1) | |||
| 7 | Chr X | 75,059,486 | 83,829,717 | C–D | — | — | L1PBa | — | — | L1MEd, L1MA1 | — | 29 NT | |||
| 8 | Chr X | 83,190,233 | 91,038,187 | D–G | TEX16P (pseudogene) | PCDH11X, intron 5 | — | — | Yes | — | — | 41 NT | |||
| 9 | Chr X | 91,089,607 | 144,762,724 | G–I | — | — | L1MB7, L1PBb, L1PA13 | Yes | — | LTR16B1 | — | 33 NT |
[i] (Chr) Chromosome; (Pos) position; (bp) base pairs; (NT) nontemplated; (NA) not applicable; (MMBIR) microhomology-mediated break-induced replication; (MMEJ) microhomology-mediated end joining.
[ii] Positions marked in bold indicate the breakpoint in sequence is not present in GRCh38 (Bilgrav Saether et al. 2024). The size of each segment is available in Supplemental Table S2.
[iii] aAmbiguous position.
[iv] bComplex mechanism.