Table 3. Genome-wide sequence context of mitomycin C-induced deletions identified by Pindel.
| Origin of Deletion | Method of Initial Detection | Deletion Size (bp) | Sequencea |
|---|---|---|---|
| h2727 | Pindel | 2 | TTCTTTTCATTTCTCtaTGTTTGCCTATCACT |
| h2758 | Pindel | 4 | TAATTTCACTGGAAtcatTGTCTTCCTTATCAC |
| h2718 | Pindel | 4 | ATCCAATTTTCCGCcgcgCAGTCGCCAAAAAGG |
| h2755 | Pindel | 5 | TAAATGACTACTgtaacGCTTGTGTCGATTTA |
| h2718 | Pindel | 5 | TTCTAGGCATATattgcGAAATATCTTTATAA |
| h2718 | Pindel | 5 | CTTGCGTGGGACCAgtcgtGTGGTCGAAACAGAC |
| h2718 | Pindel | 5 | CAAATTGGAATGCTGccgaaCTCTTGCCCATGTCT |
| h2733 | Pindel | 6 | TTTGGAGCTGTCGAcacgttCCGCGCCGCACTATA |
| h2733 | Pindel | 7 | CATAAATCGCAAActgcgttCTTCAGCAACAATAT |
| h2733 | IGV | 8 | ATTTTCTGGTGAGTGacgcgataAAATCAATATTTTCT |
| h2787 | Pindel | 8 | ATATTCGTGAAGAcattgttcCAACGCTGCACAATT |
| h2718 | Pindel | 9 | GTGACCTTAAGAAgaacgagatGAGATGGAGAGTTGA |
| h2787 | Pindel | 10 | TCCAACACAGAGAtgccgtagcgTGCAAATTAGGCTTT |
| h2718 | Pindel | 13 | ACTGCATCTGgaattccgatatcGATTTCACGATCGAA |
| h2727 | Pindel | 22 | AAAaccacgcaggcgacgcctacatACCACGCAGGCAGCC |
| h2718 | IGV | 21 | GACtcctcagcttcagcagaatacTCCTCAGCTTCAGCAGAATATCCATG |
| h2727 | Pindel | 58 | CTTTTATACGTAACCtttcc < 48 > ataaaTGAAAAATTGCTTCC |
| h2733 | Pindel | 77 | GACGACGACGAGGAAccccc < 67 > aaagcACCACGTGGAGATTA |
| h2744 | Pindel | 104 | TGTTTCAAAATATACatctg < 94 > ctaatATAAATATCCATGCC |
| h2717 | Pindel | 165 | AGtgccaacaacaatgtattc < 137 > caacaatcaTGCCAACAACAATGC |
| h2717 | Pindel | 331 | GAGGAAAAGGATAACacatt < 321 > aaaaaTCGCAAAAAACGCAT |
| h2727 | Pindel | 394 | TGGTTCGGCCAATGAatttt < 384 > ctcagTGTTTACGGTTTATA |
| h2733 | Pindel | 1003 | ATAGAGAATATACGGtatgc < 993 > gcaatTATCAGATTTCTTGT |
| h2727 | IGV | 2382 | ACATTCCTTTTCCGGggccg<2372 > tcattTTTACGCCTGTCAG |
| h2755 | IGV | 4877 | CCTCATTTTGTGTGTtaatt < 4867 > ttaatTCACTATAATCCAAA |
| h2758 | IGV | 4962 | AATATCTTCAAGCCGtcttc < 4952 > atcacCATTAAATTATTAGT |
| h2755 | Pindel | 13,671 | ATCCCACTTTGTAGAagaac < 13661 > ggagtTCCAAAGAGTCATGC |
| h2787 | IGV | 15,059 | GACAATTCGAGAGAAagaat < 15049 > ttgtgTTTGCGGAGTCGCAT |
| h2717 | IGV | 318,826 | CGTGAGTCGTTCCGAttggc < 318816 > ttcgtAGATAAAACTATTA |
a
Sequence shown includes deleted segments (underlined lower case nucleotides), flanking nucleotides (upper case nucleotides), 5′-CpG-3′ dinucleotides where visible (bolded nucleotides), and microhomology flanking the deletion junctions (double underlined nucleotides). IGV, integrative genomics viewer.