Table 3.
List of medium indels tested by PCR.
| Chr | Indel ID | Location | Ultra_contig | AF16 Amplicon (bp) | HK104 Amplicon (bp) | Predicted indel | Validation status | Validation Type | ||
|---|---|---|---|---|---|---|---|---|---|---|
| (cM) | Predicted | Observed | Predicted | Observed | ||||||
| 1 | cb-m142 | 12.6 | cb25.fpc4321 | 665 | 700 | 915 | 950 | 250 bp insertion | 250 bp insertion | * |
| cb-m2 | 13.5 | cb25.fpc4321 | 1461 | Failed PCR | 1125 | Failed PCR | 336 bp deletion | Failed PCR | ||
| cb-m5 | 20.0 | cb25.fpc4171 | 774 | 750 | 674 | Failed PCR | 100 bp deletion | Failed PCR | ||
| cb-m5 | 20.0 | cb25.fpc4171 | 461 | 500 | 361 | 500 | 100 bp deletion | no indel | ||
| cb-m6 | 43.9 | cb25.fpc4140 | 930 | 900 | 785 | 1000 | 145 bp deletion | 100 bp insertion | ** | |
| cb-m13 | unknown | cb25.fpc0078 | 504 | 420 | 385 | 400 | 119 bp deletion | 20 bp deletion | ** | |
| cb-m14 | unknown | cb25.fpc4127 | 1000 | 1000 | 676 | 710 | 324 bp deletion | 290 bp deletion | * | |
| cb-m146 | unknown | cb25.fpc4122 | 406 | 480 | 506 | 530 | 100 bp insertion | 50 bp insertion | ** | |
| cb-m12 | unknown | cb25.fpc4127 | 921 | Failed PCR | 416 | 1000 | 505 bp deletion | Failed PCR | ||
| 2 | cb-m21 | 24.2 | cb25.fpc0058 | 825 | 900 | 670 | 700 | 155 bp deletion | 200 bp deletion | * |
| cb-m16 | 37.4 | cb25.fpc4071 | 1097 | >1500 | 687 | >1500 | 410 bp deletion | unclear | ||
| cb-m19 | 11.9-13.1 | cb25.fpc0011 | 1364 | 1013 | 828 | 750 | 536 bp deletion | 263 bp deletion | ** | |
| cb-m149 | 27.9-34.0 | cb25.fpc4206 | 470 | 490 | 603 | 600 | 133 bp insertion | 110 bp insertion | * | |
| cb-m26 | 27.9-34.0 | cb25.fpc4206 | 678 | 700 | 407 | 410 | 271 bp deletion | 290 bp deletion | * | |
| cb-m38 | unknown | cb25.fpc4131 | 835 | 860 | 544 | 600 | 291 bp deletion | 260 bp deletion | * | |
| bdP4 | unknown | cb25.fpc2441 | 1013 | ~990 | 903 | ~880 | 110 bp deletion | 110 bp deletion | * | |
| 3 | cb-m46 | 6.1 | cb25.fpc2587 | 747 | 1020 | 574 | 750 | 173 bp deletion | 270 bp deletion | * |
| cb-m155 | 6.1 | cb25.fpc2587 | 1169 | Failed PCR | 1329 | Failed PCR | 160 bp insertion | Failed PCR | ||
| cb-m48 | 21.2 | cb25.fpc2976 | 1163 | 1200 | 644 | 1200 | 519 bp deletion | no indel | ||
| cb-m205 | 25.8 | cb25.fpc4079 | 671 | 700 | 971 | 1000 | 300 bp insertion | 300 bp insertion | * | |
| cb-m159 | 36.5 | cb25.fpc4224 | 463 | 500 | 655 | Failed PCR | 192 bp insertion | Failed PCR | ||
| cb-m160 | 28.8-29.3 | cb25.fpc2193 | 821 | 1000 | 1053 | 1200 | 232 bp insertion | 200 bp insertion | * | |
| bdP1 | 31.3 | cb25.fpc0002 | 1723 | ~1700 | ~1500 | ~1500 | ~200 bp deletion | 200 bp deletion | * | |
| 4 | cb-m172 | 18.2 | cb25.fpc0039 | 650 | 700 | 904 | 950 | 254 bp insertion | 250 bp insertion | * |
| cb-m170 | 20.6 | cb25.fpc4090 | 691 | 720 | 931 | Failed PCR | 240 bp insertion | Failed PCR | ||
| cb-m171 | 25.5 | cb25.fpc4132 | 381 | 450 | 476 | 550 | 95 bp insertion | 100 bp insertion | * | |
| cb-m70 | 25.5 | cb25.fpc4132 | 594 | >1600 | 421 | 1600 | 173 bp deletion | very large indel | ** | |
| cb-m176 | 37.5-41.2 | cb25.fpc3835 | 732 | Failed PCR | 1014 | Failed PCR | 282 bp insertion | Failed PCR | ||
| cb-m74 | 37.5-41.2 | cb25.fpc3835 | 677 | 1000 | 523 | 700 | 154 bp deletion | 300 bp deletion | ** | |
| cb-m76 | 42.4-43.0 | cb25.fpc2328 | 709 | 900 | 527 | 550 | 182 bp deletion | 350 bp deletion | ** | |
| cb-m177 | 9.2-9.8 | cb25.fpc4118 | 801 | 800 | 946 | 900 | 145 bp insertion | 100 bp insertion | * | |
| cb-m179 | unknown | cb25.fpc4331 | 383 | 450 | 500 | 520 | 117 bp insertion | 70 bp insertion | * | |
| 5 | cb-m103 | 19.0 | cb25.fpc2220 | 600 | 700 | 454 | 500 | 146 bp deletion | 200 bp deletion | * |
| cb-m97 | 46.1 | cb25.fpc4109 | 591 | 705 | 392 | 490 | 199 bp deletion | 215 bp deletion | * | |
| cb-m105 | 37.0-37.7 | cb25.fpc4063 | 692 | 800 | 454 | 520 | 238 bp deletion | 280 bp deletion | * | |
| cb-m104 | 37.0-37.7 | cb25.fpc4063 | 942 | Failed PCR | 661 | Failed PCR | 281 bp deletion | Failed PCR | ||
| x | cb-m197 | 3.5 | cb25.fpc4033 | 692 | 700 | 855 | 790 | 163 bp insertion | 90 bp insertion | * |
| cb-m204 | 17.4 | cb25.fpc4044 | 689 | 750 | 949 | 1000 | 260 bp insertion | 250 bp insertion | * | |
| cb-m136 | 30.1 | cb25.fpc0829 | 1440 | 2000 | 645 | 750 | 795 bp deletion | 1250 bp deletion | * | |
| cb-m127 | 34.1 | cb25.fpc2334 | 486 | 600 | 349 | 405 | 137 bp deletion | 195 bp deletion | * | |
| cb-m126 | 34.1 | cb25.fpc2334 | 785 | Failed PCR | 648 | Failed PCR | 137 bp deletion | Failed PCR | ||
| cb-m135 | 27.4-34.1 | cb25.fpc0829 | 720 | 900 | 584 | Failed PCR | 136 bp deletion | Failed PCR | ||
The indels are arranged by chromosome and location. The corresponding ultracontigs are also listed. The "unknown" locations refer to unassembled contigs. The predicted indel sizes are based on in silico analysis of AF16 and HK104 amplicons. The validation type column marks indels that were consistent with prediction (*) and those that differed significantly (**).