Spreadsheet: 00392780-4072-453a-8779-b44b615bb5e1
Sheet: S4

Table S4. Validation of 92 variants >200 bp using PCR in five DGRP lines
[NAME] worked |  |  |  |  |  | No variant predicted + PCR worked |  |  |  | [NAME] predicted
True Positive - Predicted Size (TP_PS) |  |  |  |  |  | True Negative |  |  |  | No variant predicted
True Positive - non-Predicted Size (TP_NPS) |  |  |  |  |  | [NAME]
True Positive - TP_PS + TP_NPS
False Positive
 |  |  |  |  | Category | Count |  |  | Category | Count |  |  | Category | Count |  |  | Category | Count |  |  | Category | Count
 |  |  |  |  | TP-PS |  |  |  | TP-PS |  |  |  | TP-PS |  |  |  | TP-PS |  |  |  | TP-PS
 |  |  |  |  | TN |  |  |  | TN |  |  |  | TN |  |  |  | TN |  |  |  | TN
 |  |  |  |  | TP-NPS |  |  |  | TP-NPS |  |  |  | TP-NPS |  |  |  | TP-NPS |  |  |  | TP-NPS
 |  |  |  |  | FP |  |  |  | FP |  |  |  | FP |  |  |  | FP |  |  |  | FP
 |  |  |  |  | FN |  |  |  | FN |  |  |  | FN |  |  |  | FN |  |  |  | FN
 |  |  |  |  | Failed |  |  |  | Failed |  |  |  | Failed |  |  |  | Failed |  |  |  | Failed
 |  | Line
 |  | Reference genome | DGRP-358 |  |  |  | DGRP-486 |  |  |  | DGRP-707 |  |  |  | DGRP-730 |  |  |  | DGRP-786
Variant | Type | in silico predicted PCR size (bp) | Predicted variant size (bp) | Predicted PCR size (bp) | Observed size (bp) | Category | Predicted variant size (bp) | Predicted PCR size (bp) | Observed size (bp) | Category | Predicted variant size (bp) | Predicted PCR size (bp) | Observed size (bp) | Category | Predicted variant size (bp) | Predicted PCR size (bp) | Observed size (bp) | Category | Predicted variant size (bp) | Predicted PCR size (bp) | Observed size (bp) | Category
3L:18730092 | ins, sd | 305 | 434 | 739 | empty | Failed | 0 |  | 250 | TN | 0 |  | 250-300 | TN | 0 |  | 250 | TN | 0 |  | 250 | TN
2L:18408083 | del, sd | 5031 | -4731 | 300 | 200-300 | TP-PS | -4731 |  | 250 | TP-PS | -4731 |  | 250-301 | TP-PS | -4731 |  | 250 | TP-PS | 0 |  | 250 | FN
2R:13933233 | del, sd | 521 | -299 | 222 | 200-250 | TP-PS | -299 |  | 200-250 | TP-PS | -299 |  | 250 | TP-PS | 0 |  | 200 | FN | 0 |  | 200 | FN
3R:19897868 | del, sd | 649 | -385 | 264 | 200-300 | TP-PS | -385 |  | 250 | TP-PS | -385 |  | 250 | TP-PS | 0 |  | 250 | FN | 0 |  | 250 | FN
X:7678328 | del, sd | 548 | -249 | 299 | 300 | TP-PS | 0 |  | 250-300 | FN | -249 |  | 250-300 | TP-PS | 0 |  | 300 | FN | -249 |  | 300 | TP-PS
X:13295577 | del, sd | 538 | -299 | 239 | 200-300 | TP-PS | 0 |  | 200-250 | FN | -299 |  | 250 | TP-PS | -299 |  | 700 | TP-NPS | -299 |  | 250 | TP-PS
X:18088161 | del, sd | 845 | -482 | 363 | 300-400 | TP-PS | -482 |  | 300-350 | TP-PS | -482 |  | 300 | TP-PS | -482 |  | 600 | TP-NPS | -482 |  | 200-250 | TP-NPS
2R:1336999* | ins | 229 | 338 | 567 | 400-500 | TP-NPS | 338 |  | 300-400 | TP-NPS | 338 |  | 600 | TP-PS | 338 |  | 700-800 | TP-NPS | 338 |  | 500 | TP-PS
2R:2925687 | ins | 378 | 715 | 1093 | 500-600 | TP-NPS | 715 |  | 500-600 | TP-NPS | 715 |  | 300-400 | FP | 715 |  | 600-700 | TP-NPS | 0 |  | 350 | TN
3L:4647552 | ins | 388 | 217 | 605 | 200-300 | FP | 217 |  | 300-400 | FP | 217 |  | 600 | TP-PS | 217 |  | 400 | FP | 217 |  | 600 | TP-PS
3L:5284032 | ins | 342 | 227 | 569 | 500-600 | TP-PS | 0 |  | 350-400 | TN | 227 |  | 550 | TP-PS | 0 |  | 300-400 | TN | 227 |  | 500 | TP-PS
3L:8388125 | ins | 250 | 210 | 460 | 400-500 | TP-PS | 210 |  | 250-300 | FP | 210 |  | 500 | TP-PS | 210 |  | 700 | TP-NPS | 210 |  | 450 | TP-PS
3L:8784431 | del, sd | 5627 | -5367 | 260 | 200-300 | TP-PS | 0 |  | 200-250 | FN | -5367 |  | 250 | TP-PS | -5367 |  | 500-600 | TP-NPS | -5367 |  | 250 | TP-PS
3L:13626567 | del, sd | 574 | -301 | 273 | 300 | TP-PS | 0 |  | 500-600 | TN | -301 |  | 250 | TP-PS | 0 |  | 600 | TN | 0 |  | 600 | TN
3R:4056656 | del, sd | 700 | -417 | 283 | 200-300 | TP-PS | 0 |  | 700 | TN | 0 |  | 700 | TN | 0 |  | 600-700 | TN | 0 |  | 700 | TN
3R:12847277 | del, sd | 707 | -427 | 280 | 200-300 | TP-PS | 0 |  | 700 | TN | 0 |  | 700 | TN | 0 |  | 400 | FN | 0 |  | 700 | TN
3R:15261289 | del, sd | 473 | -223 | 250 | 200-300 | TP-PS | 0 |  | 200-250 | FN | -223 |  | 250 | TP-PS | 0 |  | 400-500 | TN | 0 |  | 500 | TN
3R:16529258 | del, sd | 666 | -341 | 325 | 300-400 | TP-PS | 0 |  | 650 | TN | -341 |  | 300 | TP-PS | 0 |  | 600 | TN | 0 |  | 600 | TN
3L:16229691 | ins, sd | 224 | 0 | 224 | empty | Failed | 233 |  | empty | Failed | 0 |  | 225 | TN | 0 |  | 100-150 | FN | 0 |  | 200 | TN
2L:16280307 | del, sd | 1456 | -1115 |  | 300-400 | TP-PS | -1118 |  | 200 | TP-NPS | 0 |  | 350 | TN | 0 |  | 200 | FN | -1118 |  | 400 | TP-PS
3L:11716242 | del, sd | 4974 | -4742 | 232 | 200-250 | TP-PS | -4742 |  | 150 | TP-NPS | -4742 |  | 250 | TP-PS | -4742 |  | 100 | TP-NPS | -4742 |  | 500 | TP-NPS
3R:13417070 | del, sd | 606 | -383 | 223 | 200-300 | TP-PS | -383 |  | 100 | TP-NPS | -383 |  | 200 | TP-PS | -383 |  | 100 | TP-NPS | 0 |  | 225 | FN
3R:13588940 | del, sd | 685 | -433 | 252 | 200-250 | TP-PS | -433 |  | 150 | TP-NPS | -433 |  | 250 | TP-PS | -433 |  | 150 | TP-NPS | -433 |  | 250 | TP-PS
3R:20752907 | del, sd | 4967 | -4738 | 229 | 150-200 | TP-PS | -4738 |  | 200 | TP-PS | -4738 |  | 225 | TP-PS | -4738 |  | 200 | TP-PS | -4738 |  | 200 | TP-PS
[NAME] | del, sd | 676 | 0 | 676 | 600-700 | TN | -344 |  | 250-300 | TP-PS | 0 |  | 300 | FN | 0 |  | 250-300 | FN | 0 |  | 600 | TN
2L:4135868 | ins | 279 | 0 | 279 | 500-600 | FN | 286 |  | 500 | TP-PS | 0 |  | 500-600 | FN | 286 |  | 500 | TP-PS | 286 |  | 500 | TP-PS
3L:4934459 | ins | 314 | 0 | 314 | 400-500 | FN | 310 |  | 450 | TP-NPS | 0 |  | 300 | TN | 0 |  | 500 | FN | 0 |  | 500 | FN
3R:17502894 | ins | 259 | 261 | 520 | 500 | TP-PS | 261 |  | 500 | TP-PS | 261 |  | 500 | TP-PS | 261 |  | 500 | TP-PS | 261 |  | 500 | TP-PS
3R:18934501 | ins | 239 | 0 | 239 | 500-600 | FN | 403 |  | 600 | TP-PS | 0 |  | 300-400 | FN | 0 |  | 600 | FN | 0 |  | 600 | FN
X:10060570 | ins | 361 | 385 | 746 | 700-800 | TP-PS | 385 |  | 600-700 | TP-PS | 385 |  | 700-800 | TP-PS | 385 |  | 700 | TP-PS | 385 |  | 700 | TP-PS
X:11102799 | ins | 310 | 0 | 310 | 1000 | FN | 702 |  | 1000 | TP-PS | 0 |  | 600-700 | FN | 0 |  | 300/800 | TN | 0 |  | 1000/300 | TN
2L:13493385 | del | 462 | 0 | 462 | 300-400 | TN | -230 |  | 200-250 | TP-PS | 0 |  | 400-500 | TN | 0 |  | 400 | TN | 0 |  | 500 | TN
3L:13451072 | del, sd | 590 | 0 | 590 | 200-300 | FN | -268 |  | 250 | TP-PS | 0 |  | 500-600 | TN | 0 |  | 500 | TN | 0 |  | 300 | FN
3L:15473701 | del, sd | 660 | 0 | 660 | 500-600 | TN | -391 |  | 200-250 | TP-PS | 0 |  | 600-700 | TN | 0 |  | 500-600 | TN | 0 |  | 500 | FN
3L:17783756* | del, sd | 495 | -212 | 283 | 200-250 | TP-PS | -212 |  | 150-200 | TP-NPS | -212 |  | 250-300 | TP-PS | -212 |  | 250 | TP-PS | -212 |  | 200 | TP-PS
3R:6813052 | del, sd | 1045 | 0 | 1045 | 1000 | TN | -814 |  | 200 | TP-PS | 0 |  | 1000 | TN | 0 |  | 1000 | TN | 0 |  | 1000 | TN
3R:23295819 | del, sd | 841 | 0 | 841 | 800-900 | TN | -609 |  | 200 | TP-PS | 0 |  | 800 | TN | 0 |  | 800 | TN | -609 |  | 200 | TP-PS
2L:20976703 | del, sd | 5002 | 0 | 5002 | 200-250 | FN | 0 |  | 200 | FN | -4762 |  | 250 | TP-PS | -4762 |  | 200-250 | TP-PS | 0 |  | 200 | FN
2R:6907442* | del, sd | 5273 | 0 | 5273 | 250-300 | FN | 0 |  | 225 | FN | -5013 |  | 250 | TP-PS | 0 |  | 250 | FN | 0 |  | 200 | FN
3L:9212405 | del, sd | 971 | -619 | 352 | 200-300 | TP-PS | 0 |  | 250 | FN | -619 |  | 350 | TP-PS | -619 |  | 250-300 | TP-PS | 0 |  | 300 | FN
3L:9519644 | del, sd | 1892 | 0 | 1892 | 200-250 | FN | -1627 |  | 250 | TP-PS | -1627 |  | 250 | TP-PS | 0 |  | empty | Failed | 0 |  | 200 | FN
3R:26064541 | del, sd | 1483 | -1111 | 372 | 250-300 | TP-PS | -1111 |  | empty | Failed | -1111 |  | 350 | TP-PS | 0 |  | 350 | FN | -1111 |  | 400 | TP-PS
X:19366219* | del, sd | 748 | 0 | 748 | 200 | FN | 0 |  | 200 | FN | -517 |  | 250 | TP-PS | -517 |  | 250 | TP-PS | -517 |  | 200 | TP-PS
2L:15140409 | ins, sd | 315 | 0 | 315 | 200-250 | FN | 0 |  | 250 | TN | 424 |  | empty | Failed | 0 |  | 300 | TN | 0 |  | 300 | TN
2L:20223179 | ins | 251 | 226 | 477 | 500 | TP-PS | 226 |  | 450 | TP-PS | 226 |  | 500 | TP-PS | 226 |  | 500 | TP-PS | 226 |  | 500 | TP-PS
2R:92535 | ins | 248 | 0 | 248 | 200-250 | TN | 0 |  | 250 | TN | 388 |  | 1000 | TP-NPS | 388 |  | 200 | FP | 0 |  | 250 | TN
3R:16308873 | ins | 270 | 246 | 516 | 400-500 | TP-PS | 246 |  | 400-500 | TP-PS | 246 |  | 500 | TP-PS | 246 |  | 400-500 | TP-PS | 246 |  | 400 | TP-NPS
3R:27772929 | ins | 255 | 1430 | 1685 | 1000 | TP-NPS | 1430 |  | 900 | TP-NPS | 1430 |  | 1000 | TP-NPS | 1430 |  | 900 | TP-NPS | 1430 |  | 1000 | TP-NPS
X:3473263 | ins | 254 | 342 | 596 | 600-700 | TP-PS | 342 |  | 600 | TP-PS | 342 |  | 600 | TP-PS | 0 |  | 500-600 | FN | 342 |  | 500-600 | TP-PS
2L:2250472* | del | 1032 | -714 | 318 | 200-250 | TP-PS | -714 |  | 300 | TP-PS | -714 |  | 300 | TP-PS | 0 |  | 1000 | TN | -714 |  | 250 | TP-PS
2L:22899292 | del | 953 | 0 | 953 | 1000 | TN | 0 |  | 1000 | TN | -623 |  | 300 | TP-PS | -623 |  | 800 | FP | 0 |  | 900 | TN
3L:88799 | del, sd | 2095 | 0 | 2095 | 2000 | TN | -1867 |  | 200 | TP-PS | -1867 |  | 200 | TP-PS | -1867 |  | 2000 | FP | 0 |  | 2000 | TN
3L:5250784 | del, sd | 468 | 0 | 468 | 500 | TN | 0 |  | 450 | TN | -235 |  | 250 | TP-PS | 0 |  | 200 | FN | 0 |  | 400 | TN
3R:13172467 | del, sd | 1828 | 0 | 1828 | 550-600 | FN | -1510 |  | 300 | TP-PS | -1510 |  | 300 | TP-PS | 0 |  | 250 | FN | 0 |  | 200 | FN
3R:26726311 | del, sd | 1304 | 0 | 1304 | 200 | FN | 0 |  | 1200 | TN | -1082 |  | 200 | TP-PS | 0 |  | 1000 | FN | 0 |  | 1300 | TN
2R:871632 | ins, sd | 286 | 0 | 286 | 300/500 | TN | 306 |  | 300/600 | TP-PS | 306 |  | 700 | TP-PS | 306 |  | 250/500/800 | Failed | 306 |  | 700/200 | TP-NPS
2L:5342828 | del, sd | 2566 | 0 | 2566 | 250 | FN | -2327 |  | 200 | TP-PS | -2327 |  | 250 | TP-PS | -2327 |  | 200-250 | TP-PS | 0 |  | 250 | FN
2L:14890012 | del, sd | 605 | -372 | 233 | 200 | TP-PS | -372 |  | 200 | TP-PS | 0 |  | 600-700 | TN | -372 |  | 200-250 | TP-PS | -372 |  | 200-250 | TP-PS
2R:6867215* | del, sd | 674 | -415 | 259 | 200-250 | TP-PS | -417 |  | 250 | TP-PS | -415 |  | 250 | TP-PS | -417 |  | 200-250 | TP-PS | 0 |  | 200-250 | FN
3L:1485765 | del, sd | 1357 | 0 | 1357 | 200 | FN | 0 |  | 200 | FN | -1114 |  | 200 | TP-PS | -1114 |  | 200 | TP-PS | -1114 |  | 200 | TP-PS
3R:2563278* | del, sd | 1964 | 0 | 1964 | 200 | FN | -1734 |  | 200 | TP-PS | -1734 |  | 200 | TP-PS | -1734 |  | 200 | TP-PS | -1734 |  | 200 | TP-PS
3R:24127886 | del, sd | 640 | 0 | 640 | 200 | FN | -386 |  | 250 | TP-PS | 0 |  | 200 | FN | -386 |  | 200 | TP-PS | 0 |  | 200 | FN
2L:21335629 | ins | 339 | 0 | 339 | 300-400 | TN | 0 |  | 600 | FN | 0 |  | 300 | TN | 245 |  | 300 | FP | 492 |  | 500 | TP-NPS
2R:11464188 | ins | 258 | 0 | 258 | 500-600 | FN | 0 |  | 500 | FN | 0 |  | 500-600 | FN | 376 |  | 500-600 | TP-PS | 0 |  | empty | Failed
3L:21038647 | ins | 278 | 244 | 522 | 500-600 | TP-PS | 244 |  | 450 | TP-PS | 0 |  | 500 | FN | 244 |  | 500 | TP-PS | 244 |  | 500 | TP-PS
3R:16298431 | ins | 337 | 0 | 337 | 600-700 | FN | 271 |  | 600 | TP-PS | 0 |  | 600 | FN | 271 |  | 600 | TP-PS | 0 |  | 500 | FN
X:3673687 | ins | 308 | 464 | 772 | 700-800 | TP-PS | 464 |  | 800 | TP-PS | 464 |  | 700-800 | TP-PS | 464 |  | 300 | FP | 464 |  | 700 | TP-PS
X:5942951 | ins | 279 | 200 | 479 | 300 | FP | 200 |  | 300 | FP | 200 |  | 300-400 | TP-PS | 200 |  | 200-250 | FP | 200 |  | 350 | TP-NPS
2L:1883475 | del | 808 | 0 | 808 | 800 | TN | 0 |  | 800 | TN | -527 |  | 250-300 | TP-PS | -527 |  | 250-300 | TP-PS | 0 |  | 800 | TN
2R:1210189* | del, sd | 648 | 0 | 648 | 600-700 | TN | 0 |  | 700 | TN | -359 |  | 300 | TP-PS | -359 |  | 250-300 | TP-PS | 0 |  | 700 | TN
3L:4658021 | del, sd | 740 | 0 | 740 | 700-800 | TN | -409 |  | 300 | TP-PS | 0 |  | 700 | TN | -409 |  | 600-700 | FP | 0 |  | 700 | TN
3L:9507729 | del, sd | 494 | 0 | 494 | empty | Failed | 0 |  | 500 | TN | 0 |  | 400-500 | TN | -244 |  | 400-500 | FP | 0 |  | 500 | TN
3R:957075 | del, sd | 602 | 0 | 602 | 500-600 | TN | 0 |  | 600 | TN | 0 |  | 600 | TN | -308 |  | 500-600 | FP | 0 |  | 600 | TN
3R:5201140 | del, sd | 661 | 0 | 661 | 600-700 | TN | 0 |  | 600-700 | TN | 0 |  | 600 | TN | -369 |  | 600 | FP | 0 |  | 300 | TN
3L:17639837 | ins, sd | 269 | 0 | 269 | 600-700 | FN | 0 |  | 250 | TN | 0 |  | 250-300 | TN | 0 |  | 250 | TN | 281 |  | 400 | TP-NPS
2L:20835862 | del, sd | 994 | 0 | 994 | 200-300 | FN | 0 |  | 450 | FN | -664 |  | 200-250 | TP-PS | 0 |  | 300 | FN | -664 |  | 300 | TP-PS
3L:3281499* | del, sd | 727 | -443 | 284 | 200-300 | TP-PS | -443 |  | 250 | TP-PS | -443 |  | 250-300 | TP-PS | -443 |  | 250 | TP-PS | -443 |  | 250-300 | TP-PS
3L:19002002 | del, sd | 506 | -285 | 221 | 200-300 | TP-PS | -285 |  | 200 | TP-PS | -285 |  | 200-250 | TP-PS | -285 |  | 200 | TP-PS | -285 |  | 200 | TP-PS
3L:21630748 | del, sd | 574 | -292 | 282 | 200-300 | TP-PS | 0 |  | 600 | TN | -292 |  | 250-300 | TP-PS | 0 |  | 400 | TN | -292 |  | 250-300 | TP-PS
3R:4533136 | del, sd | 2614 | 0 | 2614 | 200-300 | FN | 0 |  | 250 | FN | -2388 |  | 200 | TP-PS | -2388 |  | 200 | TP-PS | -2388 |  | 200 | TP-PS
2L:19796933 | ins | 223 | 212 | 435 | 200-300 | FP | 0 |  | 350 | FN | 212 |  | 300 | TP-NPS | 212 |  | 300 | TP-NPS | 212 |  | 300 | TP-NPS
2L:21360458 | ins | 329 | 0 | 329 | empty | Failed | 0 |  | 300 | TN | 0 |  | 300-350 | TN | 0 |  | 300 | TN | 325 |  | empty | Failed
2R:949842 | ins | 225 | 0 | 225 | 300-400 | FN | 0 |  | 200 | TN | 0 |  | 200-250 | TN | 0 |  | 200 | TN | 306 |  | 350 | TP-NPS
2R:20409177 | ins | 232 | 258 | 490 | 500 | TP-PS | 0 |  | 200 | TN | 258 |  | 500 | TP-PS | 258 |  | 450 | TP-PS | 258 |  | 500 | TP-PS
3L:19378244** | ins | 221 | 0 | 221 | 200-300 | TN | 0 |  | 200 | TN | 0 |  | 200-250 | TN | 0 |  | 300 | TN | 210 |  | 300 | TP-NPS
X:10051013 | ins | 357 | 202 | 559 | 500-600 | TP-PS | 202 |  | 500 | TP-PS | 202 |  | 500 | TP-PS | 0 |  | 350-400 | TN | 202 |  | 500 | TP-PS
2L:22445646 | del | 660 | 0 | 660 | 300-400 | FN | -301 |  | 300 | TP-PS | 0 |  | 600 | TN | 0 |  | 300 | FN | -301 |  | 350 | TP-PS
2R:508925 | del, sd | 735 | -437 | 298 | 300 | TP-PS | 0 |  | empty | Failed | 0 |  | 700-800 | TN | 0 |  | 200-250 | FN | -437 |  | 250 | TP-PS
2R:1012809 | del, sd | 484 | -261 | 223 | 200-300 | TP-PS | -261 |  | 200 | TP-PS | -261 |  | 225 | TP-PS | 0 |  | 200 | FN | -261 |  | 200 | TP-PS
3L:8213463 | del, sd | 475 | 0 | 475 | 500 | TN | 0 |  | 500 | TN | 0 |  | 400-500 | TN | 0 |  | 450 | TN | -236 |  | 200-250 | TP-PS
3L:9102907 | del, sd | 786 | 0 | 786 | 700-800 | TN | 0 |  | 700 | TN | 0 |  | 700-800 | TN | 0 |  | 600 | FN | -552 |  | 200-250 | TP-PS
X:12734005 | del, sd | 512 | 0 | 512 | 500-600 | TN | 0 |  | 500 | TN | 0 |  | 500 | TN | 0 |  | 500 | TN | -272 |  | 200-250 | TP-PS
*Indel breakpoints validated by Sanger sequencing
**Indel breakpoints not validated by Sanger sequencing