Table 2.
Junction characteristics of identified inversions (T2T-CHM13)
| Sample ID | Size (Mbp); % Chr | Chr | PosA | PosB | Microhomology | Insertion | Junction indels pos A | Junction indels pos B | Gene posA | Gene posB | Repeat pos A | Repeat pos B | Likely mechanism jntc1/jnct2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RD_P525 | 85; 47% | 5 | 42125501 | 127429118 | 1 | – | 5 bp del | 8 bp del | OXCT1 (NM_000436.4), intron 1 | MARCHF3 (NM_178450.5), intron 3 | – | L1PA3 | NHEJ |
| 42125495 | 127429109 | – | RIns 32nt Tins 17nt |
||||||||||
| P4855_501 | 43; 25% | 6 | 51032755 | 94376921 | 2 | – | 8 bp dup | 2 bp del | – | – | AluJb, L1MA9, L1PA3 | L1PA4, LTR:MLT1J2 | MMEJ |
| 51032765 | 94376918 | 3 | – | ||||||||||
| BH16643-1 | 73–101; 53%–73% | 9 | 48424795–77056693 | 150079672 | 2 | – | – | 4 bp del | – | EHMT1 (NM_001354263.2), intron 25 | (ATTC)n | L1M5 | MMEJ |
| 48424795–77056693 | 150079676 | 3 | – | ||||||||||
| P4855_106 | 53; 40% | 10 | 42197576–42315905 | 96022615 | – | – | – | 14 bp del | – | – | (ATGG)n, (ATGGA)n, (TGGAA)n | L1MB3 | NHEJ |
| 42197576–42315905 | 96022600 | – | – | ||||||||||
| RD_P541 | 25; 19% | 12 | 32945545 | 58051150 | 2 | – | 6 bp dup | 6 bp dup | – | – | Tigger1, L1Ba | – | MMEJ |
| 32945540 | 58051144 | 1 | – | ||||||||||
| RD_P549 | 34; 32% | 14 | 63951601 | 97962156 | 3 | – | 8 bp del | 5 bp dup | SRSF5, intron 1 | ZFYVE21 (NM_001198953.2), intron 1 | L1MC5a, AluY, MER4A1 | – | MMEJ |
| 63951610 | 97962152 | 1 | – | ||||||||||
| RD_P526 | 41; 50% | 18 | 7340601 | 47883888 | 2 | – | 2 bp dup | 2 bp dup | – | LOC105372100 | – | MIR/L2 | MMEJ |
| 7340602 | 47883889 | 2 | – | ||||||||||
| RD_P542 | 48; 82% | 19 | 9982025 | 58312124 | – | TIns 23nt | 1 bp dup | 335 bp del | OLFM2 (NM_001304347.2), intron 5 | AC010327.5, intron 1 | L2b | (AT)n, AluJb, LT1B | MMBIR |
| 9982025 | 58312461 | 2 | – | ||||||||||
| RD_P546 | 49; 84% | 19 | 3256970 | 56644686 | – | RIns 90nt | – | – | CELF5 (NM_001172673.2), intron 6 | ZNF331 (NM_018555.6), intron 2 | L1ME3 | L2b | Complex MMBIR |
| 56603650 | 61454533 | 2 | – | – | – | ZNF331 (NM_001317120.2), intron 1 | ZNF497 (NM_001207009.2), intron 1 | L1PA6 | – | ||||
| 11999009 | 61440737 | – | RIns 61nt | – | – | ZNF439, intron 1 | – | – | AluY, L1MEf | ||||
| 3281277 | 6700567 | – | RIns 18nt | – | – | AC010649.1, intron 1 | C3, (NM_000064.4), exon 12 | SINE/MIRB | – | ||||
| 6755880 | 12044892 | – | RIns 16nt | – | – | SH2D3A, (NM_001386583.1), intron 1 | ZNF69 | L2a | MER92b;LTR |
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Each row represents a junction, and characteristics such as size, junction dup/dels, genes, repeats, insertions, and microhomology are given.
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(FoSTeS/MMBIR) fork stalling and template switching/microhomology-mediated break-induced replication, (NHEJ) nonhomologous end joining, (MMEJ) microhomology-mediated end joining, (NAHR) nonallelic homologous recombination, (RIns) random insertion, (Tins) templated insertion.
