Table 1.
Experimental evaluation of CHILD sensitivity and reproducibility
| % Δ construct | Predicted |
% Δ construct | Predicted |
||||
|---|---|---|---|---|---|---|---|
| P-value | Loc | Size | P-value | Loc | Size | ||
| Plasmid pMitA | |||||||
| 0 | 1E-111 | 421–423 | 2a | 15 | 8E-168 | 315–366 | 51 |
| NA | NA | NA | 2E-29 | 301–352 | 51 | ||
| 1E-99 | 183–184 | 1a | 1E-99 | 23–24 | 1a | ||
| 2.5 | NA | NA | NA | 20 | 1E-29 | 321–372 | 51 |
| 2E-68 | 354–405 | 51 | 6E-36 | 321–372 | 51 | ||
| 1E-99 | 105–106 | 1a | 1E-99 | 292–344 | 52 | ||
| 5 | 4E-129 | 319–370 | 51 | 25 | 2E-33 | 313–364 | 51 |
| 7E-140 | 323–374 | 51 | 7E-179 | 321–372 | 51 | ||
| 2E-10 | 312–363 | 51 | 1E-99 | 308–360 | 52 | ||
| 7.5 | 4E-19 | 317–368 | 51 | 30 | 1E-158 | 320–371 | 51 |
| 4E-19 | 310–361 | 51 | 4E-161 | 323–374 | 51 | ||
| 4E-27 | 320–371 | 51 | 1E-99 | 293–345 | 52 | ||
| 10 | 3E-25 | 321–372 | 51 | 50 | 2E-29 | 323–374 | 51 |
| 2E-23 | 323–374 | 51 | 6E-47 | 389–440 | 51 | ||
| 6E-129 | 304–356 | 52 | 3E-29 | 410–461 | 51 | ||
| % Δ construct | primer used: T7 | % Δ construct | primer used: SP6 | ||||
|---|---|---|---|---|---|---|---|
| Predicted |
Predicted |
||||||
| P-value | Loc | Size | P-value | Loc | Size | ||
| Plasmid pMitB | |||||||
| 5 | 1E-99 | 78–80 | 2a | 5 | 1E-99 | 44–46 | 2a |
| 1E-99 | 100–102 | 2a | 1E-99 | 22–24 | 2a | ||
| 9E-149 | 105–107 | 2a | 1E-99 | 21–23 | 2a | ||
| 10 | 1E-99 | 550–559 | 9 | 10 | 1E-99 | 22–24 | 2a |
| 1E-99 | 550–559 | 9 | 1E-99 | 31–33 | 2a | ||
| 1E-99 | 185–194 | 9 | 1E-99 | 22–24 | 2a | ||
| 15 | 1E-99 | 540–549 | 9 | 15 | 1E-99 | 32–34 | 2a |
| 1E-99 | 547–556 | 9 | 1E-99 | 46–48 | 2a | ||
| 1E-99 | 547–556 | 9 | 1E-99 | 23–25 | 2a | ||
| 20 | 1E-99 | 542–551 | 9 | 20 | 1E-99 | 423–432 | 9 |
| 1E-99 | 497–506 | 9 | 1E-99 | 206–215 | 9 | ||
| 1E-99 | 191–200 | 9 | 1E-99 | 195–204 | 9 | ||
The table shows an analysis of the 51- and 9-bp deletion constructs with CHILD.
(Upper part) Results for pMitA and pMitAΔ51.
Analysis was conducted for chromatograms generated with increasing concentration of the deletion-containing construct (%Δconstruct) and with two different sequencing primers (T7 and SP6).
The confidence that the indel is not the result of noise (P-value), the indel positions in the corresponding ABI trace file (LOC) and the inferred length of the indel (size) are given as provided by CHILD, analyzing each biological replication separately.
(lower part) The same analysis as in upper part, using pMitB and pMitBΔ9.
NA: no indel was found in the corresponding ABI trace file (the alignment was statistically insignificant or otherwise incompatible with an indel).
aIndels of length 1–2 bp are likely to be artificial (see text) and are ignored in subsequent analysis.