TABLE 1.
Rearrangement and deletion junction positions and counts for BKPyV DVGs as detected by Geneious Prime using a threshold of at least 10 reads and frequency >10% compared to maximum depth
| Sample | Junction type | Nucleotide start position | Nucleotide end position | Length (bp) | No. of Junction reads | Reads with junction (%) | Genes affected |
|---|---|---|---|---|---|---|---|
| UBK007 | Rearrangement | 268 | 4628 | 763 | 958 | 26.0 | LargeT, SmallT |
| Rearrangement | 2805 | 5068 | 2,262 | 898 | 24.3 | LargeT, SmallT | |
| Deletion | 236 | 346 | 110 | 312 | 8.5 | None | |
| Deletion | 260 | 346 | 86 | 94 | 2.6 | None | |
| Deletion | 275 | 428 | 153 | 67 | 1.8 | Agnoprotein | |
| Deletion | 317 | 324 | 7 | 45 | 1.2 | None | |
| Rearrangement | 262 | 4794 | 591 | 26 | 0.7 | Agnoprotein, LargeT, SmallT | |
| Deletion | 2914 | 3826 | 912 | 25 | 0.7 | LargeT | |
| UBK024 | Deletion | 1739 | 1746 | 7 | 546 | 25.0 | VP1 |
| Deletion | 4841 | 4971 | 130 | 320 | 14.6 | LargeT, SmallT | |
| Rearrangement (inversion) | 3059 | 4950 | 1,891 | 196 | 9.0 | LargeT, SmallT | |
| Rearrangement (inversion) | 61 | 3155 | 2,045 | 148 | 6.8 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 4647 | 4768 | 121 | 137 | 6.3 | SmallT | |
| Rearrangement (inversion) | 243 | 3354 | 2,028 | 97 | 4.4 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 76 | 4567 | 649 | 95 | 4.3 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement (inversion) | 47 | 306 | 259 | 78 | 3.6 | None | |
| Rearrangement (inversion) | 3060 | 4974 | 1,914 | 77 | 3.5 | LargeT, SmallT | |
| Deletion | 5119 | 218 | 510 | 72 | 3.3 | LargeT, SmallT | |
| Rearrangement | 611 | 405 | 207 | 51 | 2.3 | All | |
| Rearrangement | 5011 | 4981 | 31 | 43 | 2.0 | All | |
| Rearrangement | 165 | 2215 | 2,049 | 27 | 1.2 | Agnoprotein, VP1, VP2, VP3 | |
| UBK062 | Rearrangement | 272 | 5108 | 292 | 2,696 | 18.3 | All |
| Rearrangement | 49 | 2896 | 2,281 | 1,800 | 12.2 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 3074 | 4953 | 1,878 | 1,123 | 7.6 | LargeT, SmallT | |
| Deletion | 2894 | 3272 | 378 | 1,009 | 6.8 | LargeT | |
| Rearrangement | 2920 | 4168 | 1,247 | 952 | 6.5 | LargeT | |
| Rearrangement | 3272 | 49 | 1,903 | 811 | 5.5 | LargeT, SmallT | |
| Deletion | 3461 | 4191 | 730 | 603 | 4.1 | LargeT | |
| Rearrangement | 220 | 4847 | 501 | 578 | 3.9 | All | |
| Rearrangement | 327 | 5019 | 436 | 423 | 2.9 | All | |
| Rearrangement | 3325 | 4981 | 1,655 | 239 | 1.6 | LargeT, SmallT | |
| Rearrangement | 2779 | 4051 | 1,271 | 200 | 1.4 | LargeT | |
| Rearrangement | 290 | 4951 | 467 | 152 | 1.0 | All | |
| Rearrangement | 288 | 2267 | 1,978 | 116 | 0.8 | Agnoprotein, VP1, VP2, VP3 | |
| Rearrangement | 255 | 4925 | 458 | 111 | 0.8 | All | |
| Rearrangement | 303 | 4943 | 488 | 109 | 0.7 | All | |
| Deletion | 4183 | 4682 | 499 | 102 | 0.7 | LargeT, SmallT | |
| Rearrangement | 2784 | 4872 | 2,087 | 101 | 0.7 | LargeT, SmallT | |
| Deletion | 2904 | 3490 | 586 | 99 | 0.7 | LargeT | |
| Rearrangement | 480 | 2805 | 2,324 | 89 | 0.6 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 3118 | 4872 | 1,753 | 87 | 0.6 | LargeT, SmallT | |
| Rearrangement | 3634 | 4741 | 1,106 | 67 | 0.5 | LargeT, SmallT | |
| Rearrangement | 273 | 4678 | 723 | 66 | 0.5 | All | |
| Rearrangement | 285 | 4856 | 557 | 64 | 0.4 | All | |
| Rearrangement | 330 | 4962 | 496 | 47 | 0.3 | All | |
| Deletion | 3382 | 4314 | 932 | 45 | 0.3 | LargeT | |
| Deletion | 3752 | 4673 | 921 | 40 | 0.3 | LargeT, SmallT | |
| Deletion | 696 | 700 | 4 | 37 | 0.3 | VP2 | |
| Deletion | 4899 | 5098 | 199 | 36 | 0.2 | LargeT, SmallT | |
| Rearrangement | 360 | 4297 | 1,191 | 34 | 0.2 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 3037 | 2850 | 188 | 18 | 0.1 | All | |
| Rearrangement | 271 | 3065 | 2,334 | 16 | 0.1 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 307 | 692 | 385 | 15 | 0.1 | Agnoprotein, VP2 | |
| Rearrangement | 231 | 5089 | 270 | 15 | 0.1 | All | |
| Rearrangement | 391 | 4634 | 885 | 13 | 0.1 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement (inversion) | 1141 | 1179 | 38 | 13 | 0.1 | VP2, VP3 | |
| Deletion | 391 | 1047 | 656 | 12 | 0.1 | Agnoprotein, VP2, VP3 | |
| Deletion | 492 | 705 | 213 | 10 | 0.1 | Agnoprotein, VP2 | |
| UBK088 | Deletion | 2737 | 3365 | 628 | 219 | 36.4 | LargeT |
| Rearrangement | 3538 | 4935 | 1,396 | 200 | 33.2 | LargeT, SmallT | |
| Rearrangement | 277 | 4836 | 551 | 56 | 9.3 | All | |
| Rearrangement | 3379 | 245 | 1,974 | 51 | 8.5 | LargeT, SmallT | |
| Rearrangement | 3338 | 3272 | 67 | 27 | 4.5 | All | |
| UBK096 | Rearrangement (inversion) | 4736 | 4905 | 169 | 525 | 54.0 | SmallT |
| Rearrangement (inversion) | 192 | 4903 | 430 | 186 | 19.1 | All | |
| Rearrangement | 2731 | 4963 | 2,231 | 68 | 7.0 | LargeT, SmallT | |
| Rearrangement | 300 | 4650 | 792 | 48 | 4.9 | All | |
| Deletion | 183 | 322 | 139 | 31 | 3.2 | None | |
| Rearrangement (inversion) | 3780 | 3825 | 45 | 23 | 2.4 | LargeT | |
| Rearrangement | 24 | 1851 | 1,826 | 19 | 2.0 | Agnoprotein, VP1, VP2, VP3 | |
| Rearrangement | 2796 | 5043 | 2,246 | 14 | 1.4 | LargeT, SmallT | |
| Rearrangement | 4740 | 2337 | 2,404 | 12 | 1.2 | All | |
| UBK121 | Deletion | 4382 | 4558 | 176 | 6,030 | 55.7 | LargeT |
| Rearrangement (inversion) | 4208 | 5021 | 813 | 5174 | 47.8 | LargeT, SmallT | |
| Deletion | 1898 | 1902 | 4 | 3,634 | 33.5 | VP1 | |
| Deletion | 3747 | 3756 | 9 | 1,700 | 15.7 | LargeT | |
| Deletion | 3797 | 3984 | 187 | 1,587 | 14.7 | LargeT | |
| Rearrangement | 4847 | 3811 | 1,037 | 881 | 8.1 | LargeT, SmallT | |
| Rearrangement (inversion) | 4210 | 5017 | 807 | 774 | 7.1 | LargeT, SmallT | |
| Deletion | 4682 | 4855 | 173 | 753 | 7.0 | SmallT | |
| Rearrangement (inversion) | 96 | 4749 | 442 | 653 | 6.0 | All | |
| Rearrangement | 4302 | 2962 | 1,341 | 611 | 5.6 | All | |
| Rearrangement (inversion) | 4207 | 5020 | 813 | 583 | 5.4 | LargeT, SmallT | |
| Deletion | 3501 | 3511 | 10 | 486 | 4.5 | LargeT | |
| Rearrangement | 4104 | 3467 | 638 | 435 | 4.0 | All | |
| Deletion | 2843 | 3499 | 656 | 271 | 2.5 | LargeT | |
| Rearrangement | 3624 | 4989 | 1,364 | 246 | 2.3 | LargeT, SmallT | |
| Deletion | 1883 | 1890 | 7 | 196 | 1.8 | VP1 | |
| Rearrangement | 3341 | 32 | 1,785 | 171 | 1.6 | LargeT, SmallT | |
| Deletion | 4587 | 4677 | 90 | 152 | 1.4 | SmallT | |
| Rearrangement | 3461 | 3,455 | 7 | 113 | 1.0 | All | |
| Deletion | 2678 | 2686 | 8 | 99 | 0.9 | None | |
| Rearrangement (inversion) | 3097 | 5,046 | 1,949 | 83 | 0.8 | LargeT, SmallT | |
| Rearrangement (inversion) | 4818 | 5070 | 252 | 82 | 0.8 | LargeT, SmallT | |
| Rearrangement (inversion) | 3635 | 4972 | 1,337 | 69 | 0.6 | LargeT, SmallT | |
| Rearrangement (inversion) | 4313 | 4817 | 504 | 63 | 0.6 | LargeT, SmallT | |
| Rearrangement (inversion) | 2770 | 4570 | 1,800 | 51 | 0.5 | LargeT | |
| Rearrangement (inversion) | 3109 | 4254 | 1,145 | 50 | 0.5 | LargeT | |
| Deletion | 4,641 | 4846 | 205 | 50 | 0.5 | SmallT | |
| Deletion | 4308 | 4778 | 470 | 42 | 0.4 | LargeT, SmallT | |
| Rearrangement | 80 | 4639 | 537 | 32 | 0.3 | All | |
| Deletion | 3612 | 3616 | 4 | 29 | 0.3 | LargeT | |
| Deletion | 3550 | 4185 | 635 | 28 | 0.3 | LargeT | |
| Deletion | 664 | 668 | 4 | 26 | 0.2 | VP2 | |
| Rearrangement (inversion) | 155 | 4625 | 625 | 26 | 0.2 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement (inversion) | 4694 | 4727 | 33 | 26 | 0.2 | SmallT | |
| Rearrangement (inversion) | 3153 | 3984 | 831 | 24 | 0.2 | LargeT | |
| Deletion | 4788 | 4794 | 6 | 22 | 0.2 | SmallT | |
| Rearrangement (inversion) | 3594 | 4299 | 705 | 21 | 0.2 | LargeT | |
| Deletion | 4,694 | 4704 | 10 | 19 | 0.2 | SmallT | |
| Deletion | 4888 | 5094 | 206 | 18 | 0.2 | LargeT, SmallT | |
| Rearrangement (inversion) | 24 | 4273 | 846 | 18 | 0.2 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| UBK161 | Rearrangement | 2686 | 4944 | 2,257 | 1,369 | 25.6 | LargeT, SmallT |
| Rearrangement | 501 | 2259 | 1,757 | 426 | 8.0 | All | |
| Rearrangement | 2246 | 5041 | 2,318 | 82 | 1.5 | LargeT, SmallT, VP1 | |
| Deletion | 3476 | 3509 | 33 | 29 | 0.5 | LargeT | |
| Rearrangement | 472 | 1707 | 1,234 | 28 | 0.5 | Agnoprotein, VP1, VP2, VP3 | |
| Rearrangement (inversion) | 320 | 340 | 20 | 20 | 0.4 | None | |
| Deletion | 681 | 685 | 4 | 14 | 0.3 | VP2 | |
| Rearrangement | 5094 | 1970 | 1,987 | 14 | 0.3 | All | |
| UBK178 | Rearrangement | 400 | 4922 | 620 | 1,099 | 20.6 | All |
| Deletion | 2931 | 3865 | 934 | 952 | 9.5 | LargeT | |
| Rearrangement (inversion) | 288 | 3478 | 1,951 | 601 | 6.0 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement (inversion) | 4638 | 5037 | 399 | 590 | 5.9 | LargeT, SmallT | |
| Deletion | 5079 | 365 | 530 | 34 | 0.3 | LargeT, SmallT | |
| Deletion | 710 | 714 | 4 | 32 | 0.3 | VP2 | |
| Rearrangement (inversion) | 2633 | 2711 | 78 | 31 | 0.3 | VP1 | |
| Rearrangement | 353 | 293 | 61 | 27 | 0.3 | All | |
| Rearrangement | 2413 | 4899 | 2,485 | 22 | 0.2 | LargeT, SmallT, VP1 | |
| Rearrangement (inversion) | 3199 | 3356 | 157 | 22 | 0.2 | LargeT | |
| Rearrangement | 478 | 1,534 | 1,055 | 19 | 0.2 | Agnoprotein, VP2, VP3 | |
| Deletion | 2488 | 2,502 | 14 | 18 | 0.2 | VP1 | |
| Deletion | 158 | 301 | 143 | 16 | 0.2 | None | |
| Rearrangement (inversion) | 1838 | 2150 | 312 | 16 | 0.2 | VP1 | |
| Rearrangement | 66 | 4748 | 460 | 15 | 0.2 | All | |
| Rearrangement (inversion) | 1453 | 1463 | 10 | 14 | 0.1 | VP2, VP3 | |
| Rearrangement (inversion) | 137 | 4957 | 321 | 14 | 0.1 | All | |
| Rearrangement (inversion) | 2808 | 3360 | 552 | 13 | 0.1 | LargeT | |
| Deletion | 3446 | 3458 | 12 | 11 | 0.1 | LargeT | |
| Deletion | 477 | 583 | 106 | 10 | 0.1 | Agnoprotein | |
| UBK264 | Rearrangement | 2359 | 4814 | 2,454 | 14 | 7.0 | LargeT, SmallT, VP1 |
| Rearrangement | 276 | 1892 | 1,615 | 12 | 6.0 | Agnoprotein, VP1, VP2, VP3 | |
| UBK265 | Rearrangement | 2964 | 4702 | 1,737 | 553 | 5.5 | LargeT, SmallT |
| Rearrangement | 203 | 2891 | 2,454 | 305 | 3.0 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 304 | 2360 | 2,055 | 215 | 2.1 | Agnoprotein, VP1, VP2, VP3 | |
| Rearrangement | 2622 | 4703 | 2,080 | 104 | 1.0 | LargeT, SmallT, VP1 | |
| Deletion | 270 | 311 | 41 | 87 | 0.9 | None | |
| Rearrangement | 3827 | 4873 | 1,045 | 65 | 0.6 | LargeT, SmallT | |
| Rearrangement | 3429 | 4755 | 1,325 | 52 | 0.5 | LargeT, SmallT | |
| Rearrangement (inversion) | 3894 | 4519 | 625 | 50 | 0.5 | LargeT | |
| Rearrangement (inversion) | 275 | 4495 | 921 | 49 | 0.5 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 710 | 714 | 4 | 49 | 0.5 | VP2 | |
| Deletion | 180 | 354 | 174 | 49 | 0.5 | None | |
| Rearrangement | 282 | 2741 | 2,458 | 42 | 0.4 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 230 | 3539 | 1,833 | 39 | 0.4 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 3813 | 5001 | 1,187 | 37 | 0.4 | LargeT, SmallT | |
| Rearrangement | 218 | 3599 | 1,761 | 32 | 0.3 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 3867 | 4649 | 782 | 32 | 0.3 | LargeT, SmallT | |
| Deletion | 3019 | 3925 | 906 | 30 | 0.3 | LargeT | |
| Rearrangement | 3733 | 5104 | 1,370 | 27 | 0.3 | LargeT, SmallT | |
| Rearrangement | 282 | 3837 | 1,587 | 26 | 0.3 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 263 | 2914 | 2,491 | 26 | 0.3 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 281 | 4554 | 869 | 26 | 0.3 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 498 | 517 | 19 | 25 | 0.3 | Agnoprotein | |
| Rearrangement | 261 | 4826 | 577 | 25 | 0.3 | All | |
| Deletion | 252 | 349 | 97 | 25 | 0.3 | None | |
| Rearrangement | 263 | 4455 | 950 | 24 | 0.2 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 227 | 4703 | 666 | 24 | 0.2 | All | |
| Rearrangement | 266 | 4703 | 705 | 24 | 0.2 | All | |
| Rearrangement (inversion) | 31 | 390 | 359 | 21 | 0.2 | Agnoprotein | |
| Rearrangement | 280 | 4771 | 651 | 19 | 0.2 | All | |
| Rearrangement | 3100 | 4491 | 1,390 | 15 | 0.2 | LargeT | |
| Deletion | 252 | 357 | 105 | 14 | 0.1 | None | |
| UBK266 | Rearrangement | 251 | 4712 | 681 | 83 | 3.4 | All |
| Rearrangement (inversion) | 13 | 307 | 294 | 69 | 2.8 | None | |
| Rearrangement | 3643 | 4721 | 1,077 | 48 | 2.0 | LargeT, SmallT | |
| Rearrangement | 313 | 4610 | 845 | 42 | 1.7 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Rearrangement | 260 | 4703 | 699 | 38 | 1.6 | All | |
| Rearrangement | 312 | 4931 | 523 | 37 | 1.5 | All | |
| Rearrangement | 301 | 4778 | 665 | 32 | 1.3 | All | |
| Rearrangement (inversion) | 1857 | 5048 | 1,950 | 28 | 1.2 | LargeT, SmallT, VP1 | |
| Rearrangement | 2862 | 5129 | 2,266 | 27 | 1.1 | LargeT, SmallT | |
| Rearrangement | 324 | 4443 | 1,023 | 26 | 1.1 | Agnoprotein, LargeT, VP1, VP2, VP3 | |
| Deletion | 4851 | 5007 | 156 | 23 | 0.9 | LargeT, SmallT | |
| Rearrangement | 337 | 2519 | 2,181 | 23 | 0.9 | Agnoprotein, VP1, VP2, VP3 | |
| Deletion | 1976 | 2481 | 505 | 22 | 0.9 | VP1 | |
| Rearrangement | 1837 | 4991 | 1,988 | 20 | 0.8 | LargeT, SmallT, VP1 | |
| Deletion | 3937 | 4869 | 932 | 17 | 0.7 | LargeT, SmallT | |
| Rearrangement | 232 | 1615 | 1,382 | 12 | 0.5 | Agnoprotein, VP1, VP2, VP3 | |
| UBK282 | Deletion | 4421 | 4597 | 176 | 2,175 | 30.0 | LargeT |
| Deletion | 1937 | 1941 | 4 | 1,290 | 17.8 | VP1 | |
| Rearrangement (inversion) | 4247 | 5060 | 813 | 1,076 | 14.8 | LargeT, SmallT | |
| Deletion | 3781 | 3790 | 9 | 545 | 7.5 | LargeT | |
| Deletion | 3831 | 4018 | 187 | 503 | 6.9 | LargeT | |
| Rearrangement (inversion) | 4250 | 5057 | 807 | 475 | 6.6 | LargeT, SmallT | |
| Rearrangement | 4886 | 3850 | 1,037 | 422 | 5.8 | All | |
| Rearrangement (inversion) | 95 | 4789 | 440 | 381 | 5.3 | All | |
| Deletion | 2882 | 3538 | 656 | 294 | 4.1 | LargeT | |
| Deletion | 762 | 766 | 4 | 290 | 4.0 | VP2 | |
| Rearrangement | 3663 | 5028 | 1,364 | 247 | 3.4 | LargeT, SmallT | |
| Deletion | 3540 | 3550 | 10 | 220 | 3.0 | LargeT | |
| Deletion | 1922 | 1929 | 7 | 191 | 2.6 | VP1 | |
| Rearrangement | 4143 | 3506 | 638 | 188 | 2.6 | All | |
| Rearrangement (inversion) | 4246 | 5059 | 813 | 156 | 2.2 | LargeT, SmallT | |
| Rearrangement (inversion) | 4249 | 5056 | 807 | 135 | 1.9 | LargeT, SmallT | |
| Rearrangement | 4341 | 3001 | 1,341 | 134 | 1.9 | All | |
| Deletion | 4721 | 4894 | 173 | 130 | 1.8 | SmallT | |
| Rearrangement (inversion) | 2785 | 2859 | 74 | 79 | 1.1 | LargeT | |
| Deletion | 4626 | 4716 | 90 | 58 | 0.8 | SmallT | |
| Rearrangement | 3500 | 3494 | 7 | 52 | 0.7 | All | |
| Rearrangement (inversion) | 2764 | 5058 | 2,294 | 41 | 0.6 | LargeT, SmallT | |
| Deletion | 4364 | 4788 | 424 | 26 | 0.4 | LargeT, SmallT | |
| Rearrangement (inversion) | 4857 | 5109 | 252 | 23 | 0.3 | LargeT, SmallT | |
| Deletion | 4420 | 4610 | 190 | 20 | 0.3 | LargeT | |
| Deletion | 540 | 553 | 13 | 19 | 0.3 | Agnoprotein | |
| Rearrangement | 4665 | 3510 | 1,156 | 18 | 0.3 | All | |
| Rearrangement | 23 | 5122 | 36 | 15 | 0.2 | All | |
| UBK007—using Kapa HyperPrep Plus kit | Rearrangement | 2805 | 5068 | 2,262 | 98 | 17.92 | LargeT, SmallT |
| Rearrangement | 268 | 4628 | 763 | 90 | 16.45 | All | |
| Deletion | 236 | 346 | 110 | 43 | 7.86 | None | |
| Deletion | 275 | 428 | 153 | 20 | 3.66 | Agnoprotein | |
| UBK096—using Kapa HyperPrep Plus kit | Rearrangement (inversion) | 192 | 4903 | 430 | 44 | 41.9 | All |
| Rearrangement (inversion) | 4736 | 4905 | 169 | 35 | 33.33 | LargeT, SmallT |