| Organism | Assembly method | Library preparation method | Starting DNA quantity, ng | # of contigs | Total bps | Relative to the reference genomes | Deletions | Insertions | Total indels | Rearrangements |
| B. anthracis | Allpaths | NEBNext | 100 | 21 | 5,358,817 | 170 | 6,518 | 6,688 | 80 | TruSeq | 1000 | 23 | 5,348,296 | 170 | 50,762 | 50,932 | 92 | IDBA | NEBNext | 100 | 48 | 5,349,320 | 1,525 | 16,827 | 18,352 | 102 | TruSeq | 1000 | 41 | 5,483,709 | 87,019 | 1,838 | 88,857 | 104 |
| E. coli | Allpaths | NEBNext | 100 | 82 | 5,312,046 | 758 | 48,753 | 49,511 | 222 | TruSeq | 1000 | 96 | 5,269,849 | 760 | 80,227 | 80,987 | 238 | IDBA | NEBNext | 100 | 199 | 5,216,101 | 111 | 152,190 | 152,301 | 414 | TruSeq | 1000 | 207 | 5,242,710 | 224 | 75,926 | 76,150 | 446 |
| B. thailandensisā
A
| Allpaths | NEBNext | 10 | 26 | 6,652,405 | 100 | 12,213 | 12,313 | 80 | NEBNext | 100 | 27 | 6,650,888 | 143 | 13,042 | 13,185 | 154 | TruSeq | 1000 | 77 | 6,603,636 | 6,294 | 27,237 | 33,531 | 252 | IDBA | NEBNext | 10 | 119 | 6,575,406 | 206 | 38,419 | 38,625 | 276 | NEBNext | 100 | 117 | 6,575,500 | 351 | 38,382 | 38,733 | 280 | TruSeq | 1000 | 271 | 6,582,658 | 8,320 | 35,337 | 43,657 | 586 |
| B. thailandensisā
B
| Allpaths | NEBNext | 10 | 23 | 6,660,010 | 144 | 12,576 | 12,720 | 82 | NEBNext | 100 | 27 | 6,651,385 | 163 | 12,278 | 12,441 | 86 | TruSeq | 1000 | 53 | 6,655,446 | 157 | 16,517 | 16,674 | 204 | IDBA | NEBNext | 10 | 129 | 6,579,849 | 749 | 45,201 | 45,950 | 264 | NEBNext | 100 | 125 | 6,579,749 | 236 | 44,279 | 44,515 | 262 | TruSeq | 1000 | 281 | 6,587,931 | 8,694 | 45,997 | 54,691 | 612 |
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