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Table 3 List of medium indels tested by PCR.

From: A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

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  
  1. 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 (**).